Biomedical subjects

Gregory M Cooper

Publications and source records attributed to Gregory M Cooper.

18 recordsLinked to original sources

PubMed2006

VEGF and BMP expression in mouse osteosarcoma cells.

Osteosarcoma is the most common primary bone malignancy. Despite improvements in therapy, approximately 30% of patients experience pulmonary metastasis. Expression of several growth factors, including VEGF and BMPs, has been implicated in tumor progression and metastatic potential. We hypothesized increased metastatic potential of mouse osteosarcoma cells positively correlates with the expression of VEGF and BMPs. We studied the expression patterns of these growth factors in two murine osteosarcoma cell lines with varying degrees of metastatic potential: K7M2 (highly metastatic) and K12 (minimally metastatic). Expression of VEGF and BMP2 were higher in the metastatic K7M2 cell line. We also investigated the effects of the BMP antagonist noggin on osteosarcoma growth characteristics in vitro. We noted decreased motility, altered morphology, and increased cell death in the highly metastatic K7M2 cell line. Less metastatic K12 cells showed substantial cell death without clear alteration of motility or morphology. These data suggest BMP2 expression may be an important factor in osteosarcoma metastasis and noggin administration theoretically could block its actions. Inhibition of BMPs and VEGF should be investigated further as a possible strategy for decreasing the incidence of pulmonary metastases in osteosarcoma.

Animals↗

PubMed2006

Intracranial volume changes in craniosynostotic rabbits: effects of age and surgical correction.

BACKGROUND: The premature fusion of one or more cranial sutures, termed craniosynostosis, alters normal brain growth patterns and results in compensatory changes in the cranial vault. The authors previously reported that bilateral coronal suture fusion resulted in a reduction in intracranial volume in a rabbit model of nonsyndromic, familial coronal suture synostosis. METHODS: The current follow-up study involved collecting cross-sectional three-dimensional computed tomographic head scans from 142 rabbits (70 normal, 44 with uncorrected synostosis, and 28 synostosed rabbits with coronal suturectomy) at 0, 10, 25, 42, 84, and 126 days of age. Intracranial contents were reconstructed, and indirect intracranial volume was calculated. RESULTS: Results revealed a significant (p < 0.05) postsynostotic reduction of intracranial volume (23 percent) by 25 days of age in rabbits with uncorrected craniosynostosis compared with normal controls, which continued through 84 days of age. Also, rabbits with surgically released synostosis, using a simple strip suturectomy, showed significantly (p < 0.05) greater intracranial volume at 25 days of age compared with unoperated synostosed rabbits. However, no changes in intracranial volume were noted between 42 and 84 days of age in rabbits with surgically released synostosis, at which point their intracranial volume was 30 percent less than that in normal control rabbits. CONCLUSIONS: These data suggest that in rabbits with uncorrected craniosynostosis, compensatory changes in the neurocranium were not capable of compensating for the loss of sutures as growth sites. The results also showed that that surgical release of the synostosed suture improved intracranial volume in the short term (25 to 42 days) but failed to change it in the long term (42 to 84 days), possibly because of rapid resynostosis of the suturectomy site. This study suggests that surgical release of the suture fusion site alone may not be adequate to allow for normal intracranial volume growth in synostotic rabbits. For this reason, it may be efficacious to design and develop adjunct protein and gene therapies to prevent resynostosis and improve postoperative intracranial volume in craniosynostotic individuals.

Age Factors↗

PubMed2006

Conversion Furlow palatoplasty: salvage of speech after straight-line palatoplasty and "incomplete intravelar veloplasty".

INTRODUCTION: The straight-line palatoplasty with intravelar veloplasty (IVVP) is one option for cleft palate repair. However, not all IVVPs are performed uniformly. Many IVVPs only address the medialmost portion of the levator muscle, an "incomplete IVVP," failing to completely dissect and adequately transpose the entire levator muscle, "complete IVVP." We believe that for optimal speech results, IVVPs should completely mobilize and posteriorly displace the levator. We propose that a conversion Furlow palatoplasty performed with a "complete IVVP" will correct postoperative velopharyngeal insufficiency (VPI) and alleviate the need for pharyngoplasty. METHODS: Nineteen patients with postoperative VPI, having had prior straight-line palatoplasty and reported "IVVP," underwent conversion Furlow palatoplasty. Those with a pre- and postoperative Pittsburgh Weighted Speech Scale (PWSS) value and no other history of palatal surgeries were included in this study. Statistical analysis was performed by using the Wilcoxon signed ranks test. RESULTS: Patients' median age was 5.5 years (range, 4-15 years), with 13 males and 7 females. The median preoperative PWSS score was 11.00 (range, 3-24.5), and the median postoperative was 1.00 (range, 0-5) (P < 0.001). All subcategories of the PWSS were also improved. Eight children had a preoperative fistula, and all were successfully corrected. At the time of conversion Furlow palatoplasty, all patients demonstrated no evidence of previous IVVP as the levator muscle was found to be scarred to the posterior edge of the hard palate. CONCLUSION: The conversion Furlow palatoplasty can be used to significantly improve VPI and salvage speech after a straight-line palatoplasty with an "incomplete IVVP." Patients with postoperative VPI should first be considered for conversion Furlow palatoplasty performed with a "complete IVVP" prior to progressing to pharyngoplasty.

Adolescent↗

PubMed2006

The osteogenic potential of adipose-derived stem cells for the repair of rabbit calvarial defects.

INTRODUCTION: Bone replacement is often necessary during reconstruction of craniofacial anomalies or trauma. Adipose-derived stem cells (ASCs) possess osteogenic potential and are a promising cell source for bone tissue engineering. The present study was designed to assess the osteogenic potential and utility of using ASCs to regenerate bone in a rabbit calvarial defect model. METHODS: Rabbit ASCs were seeded on gelatin foam (GF) scaffolds and induced in osteogenic medium containing bone morphogenetic protein (BMP)-2. Thirty-four 8-mm calvarial defects were randomly treated with autograft, no treatment, GF scaffold, GF + ASCs, or GF + osteoinduced ASCs. After 6 weeks, calvaria were harvested and underwent histologic and radiologic analyses to compare healing between the treatment groups. RESULTS: Defects treated with autograft underwent complete healing. Radiologically, there were no significant (P > 0.05) differences in healing among empty defects, and those treated with GF alone or GF plus osteoinduced ASCs. Osteoinduced ASCs exhibited significantly (P < 0.05) greater healing than noninduced ASCs. CONCLUSION: Preimplantation osteoinduction of ASCs enhances their osteogenic capacity. Lack of a significant osteogenic effect of ASCs on calvarial healing at 6 weeks may be secondary to use of noncritical-sized defects. Larger defects would likely demonstrate the osteogenic potential of ASCs more definitively.

Adipose Tissue↗

PubMed2006

Interviewing the incarcerated offender convicted of sexually assaulting the elderly.

Sexual assault is considered one of the most terrible crimes committed against the elderly, particularly as they are noted to be among the most innocent and vulnerable of populations. To better understand offender motivation and related behaviors, this article presents suggestions that are possible guidelines for forensic interviews, including an examination of potential methods for obtaining cooperation to optimize a truthful and accurate disclosure of offenders' crimes for research purposes.

Aged↗

PubMed2005

VEGF improves, whereas sFlt1 inhibits, BMP2-induced bone formation and bone healing through modulation of angiogenesis.

UNLABELLED: We studied the interaction between VEGF and BMP2 during bone formation and bone healing. Results indicate that VEGF antagonist inhibited BMP2-elicited bone formation, whereas the delivery of exogenous VEGF enhanced BMP2-induced bone formation and bone healing through modulation of angiogenesis. INTRODUCTION: Angiogenesis is closely associated with bone formation during normal bone development and is important for the bone formation elicited by BMP4. However, it remains unknown whether vascular endothelial growth factor (VEGF) also interacts with other BMPs, especially BMP2, in bone formation and bone healing. MATERIALS AND METHODS: For this study, mouse muscle-derived stem cells were transduced to express BMP2, VEGF, or VEGF antagonist (sFlt1). We studied the angiogenic process during endochondral bone formation elicited by BMP2, a prototypical osteogenic BMP. Using radiographic and histologic analyses, we also evaluated the interaction between VEGF and BMP2 during bone formation and bone healing. RESULTS: Our results indicate that BMP2-elicited bone formation comprises two phases of angiogenesis, with an early phase occurring before the appearance of hypertrophic cartilage, followed by a late phase coupled with the appearance of hypertrophic cartilage. Our finding that the administration of sFlt1, a specific antagonist of VEGF, significantly inhibited BMP2-induced bone formation and the associated angiogenesis indicates that endogenous VEGF activity is important for bone formation. Furthermore, we found that the delivery of exogenous VEGF enhanced BMP2-induced bone formation and bone healing by improving angiogenesis, which in turn led to accelerated cartilage resorption and enhanced mineralized bone formation. Our findings also indicate that the ratio between VEGF and BMP2 influences their synergistic interaction, with a higher proportion of VEGF leading to decreased synergism. Our study also revealed unique VEGF-BMP2 interactions that differ from the VEGF-BMP4 interactions that we have described previously. CONCLUSIONS: This study, along with previously published work, shows that VEGF interacts synergistically with both BMP4 and BMP2 but elicits substantially different effects with these two BMPs.

Animals↗

PubMed2005

Distribution and intensity of constraint in mammalian genomic sequence.

Comparisons of orthologous genomic DNA sequences can be used to characterize regions that have been subject to purifying selection and are enriched for functional elements. We here present the results of such an analysis on an alignment of sequences from 29 mammalian species. The alignment captures approximately 3.9 neutral substitutions per site and spans approximately 1.9 Mbp of the human genome. We identify constrained elements from 3 bp to over 1 kbp in length, covering approximately 5.5% of the human locus. Our estimate for the total amount of nonexonic constraint experienced by this locus is roughly twice that for exonic constraint. Constrained elements tend to cluster, and we identify large constrained regions that correspond well with known functional elements. While constraint density inversely correlates with mobile element density, we also show the presence of unambiguously constrained elements overlapping mammalian ancestral repeats. In addition, we describe a number of elements in this region that have undergone intense purifying selection throughout mammalian evolution, and we show that these important elements are more numerous than previously thought. These results were obtained with Genomic Evolutionary Rate Profiling (GERP), a statistically rigorous and biologically transparent framework for constrained element identification. GERP identifies regions at high resolution that exhibit nucleotide substitution deficits, and measures these deficits as "rejected substitutions". Rejected substitutions reflect the intensity of past purifying selection and are used to rank and characterize constrained elements. We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer.

Animals↗

PubMed2005

Secondary pneumatization of the maxillary sinus in callitrichid primates: insights from immunohistochemistry and bone cell distribution.

The paranasal sinuses remain elusive both in terms of function and in the proximate mechanism of their development. The present study sought to describe the maxillary sinuses (MSs) in three species of callitrichid primates at birth, a time when secondary pneumatization occurs rapidly in humans. The MSs were examined in serially sectioned and stained slides from the heads of two Callithrix jacchus, one Leontopithecus rosalia, and two Saguinus geoffroyi. Specimens were examined microscopically regarding the distribution of osteoclasts and osteoblasts along the osseous boundaries of the MS and other parts of the maxillary bone. Selected sections were immunohistochemically evaluated for the distribution of osteopontin (OPN), which facilitates osteoclast binding. Taken together, OPN immunoreactivity and bone cell distribution suggested trends of bone resorption/deposition that were consistent among species for the superior (roof) and inferior (floor) boundaries of the MS. Expansion at the roof and floor of the MS appeared to correspond to overall vertical midfacial growth in callitrichids. Much more variability was noted for the lateral (alveolar) and medial (nasal walls) of the MS. Unlike the other species, the nasal wall of Saguinus was static and mostly composed of inferior portions of the nasal capsule that were undergoing endochondral ossification. The variation seen in the alveolar walls may relate to the presence or absence of adjacent structures, although it was noted that adjacency of deciduous molars influenced medial drift of the alveolar wall in Saguinus but not Leontopithecus. The results of this study are largely consistent with the "structural" or "architectural" hypothesis of sinus formation with respect to vertical MS enlargement, and the variable cellular/OPN distribution found along the nasal and alveolar walls was evocative of Witmer's (J Vert Paleontol 1997;17:1-73) epithelial hypothesis in revealing that most expansion occurred in regions unopposed by adjacent structures.

Animals↗

PubMed2005

Noggin improves bone healing elicited by muscle stem cells expressing inducible BMP4.

The aim of this study was to test the hypothesis that a specific antagonist may enhance the efficacy of its corresponding growth factor in a regulated tissue engineering strategy. Our prior research has led to the development of a retroviral vector that enables optimal regulated bone morphogenetic protein 4 (BMP4) expression in vitro and regulated bone formation in vivo with transduced muscle stem cells. However, when implanted in critical-sized calvarial defects, these cells led to residual bone formation without induction or bone overgrowth with induction, even at reduced cell doses. We thus co-implanted the aforementioned cells with stem cells engineered to express Noggin, a specific BMP antagonist. This approach, while preserving our ability to regulate bone regeneration closely, prevented both the basal level bone regeneration and the bone overgrowth and, more importantly, led to the regeneration of bone that more closely resembled normal bone. We believe that this regulatable tissue engineering strategy, enhanced by utilizing a specific antagonist, constitutes a new paradigm for tissue engineering and regenerative medicine.

Adenoviridae↗

PubMed2005

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

As whole-genome sequencing efforts extend beyond more traditional model organisms to include a deep diversity of species, comparative genomic analyses will be further empowered to reveal insights into the human genome and its evolution. The discovery and annotation of functional genomic elements is a necessary step toward a detailed understanding of our biology, and sequence comparisons have proven to be an integral tool for that task. This review is structured to broadly reflect the statistical challenges in discriminating these functional elements from the bulk of the genome that has evolved neutrally. Specifically, we review the comparative genomics literature in terms of specificity, sensitivity, and phylogenetic scope, as well as the trade-offs that relate these factors in standard analyses. We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling.

Animals↗

PubMed2004

ABC: software for interactive browsing of genomic multiple sequence alignment data.

BACKGROUND: Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task. RESULTS: The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics. CONCLUSIONS: The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available http://mendel.stanford.edu/sidowlab/downloads.html.

Animals↗

PubMed2004

Characterization of evolutionary rates and constraints in three Mammalian genomes.

We present an analysis of rates and patterns of microevolutionary phenomena that have shaped the human, mouse, and rat genomes since their last common ancestor. We find evidence for a shift in the mutational spectrum between the mouse and rat lineages, with the net effect being a relative increase in GC content in the rat genome. Our estimate for the neutral point substitution rate separating the two rodents is 0.196 substitutions per site, and 0.65 substitutions per site for the tree relating all three mammals. Small insertions and deletions of 1-10 bp in length ("microindels") occur at approximately 5% of the point substitution rate. Inferred regional correlations in evolutionary rates between lineages and between types of sites support the idea that rates of evolution are influenced by local genomic or cell biological context. No substantial correlations between rates of point substitutions and rates of microindels are found, however, implying that the influences that affect these processes are distinct. Finally, we have identified those regions in the human genome that are evolving slowly, which are likely to include functional elements important to human biology. At least 5% of the human genome is under substantial constraint, most of which is noncoding.

Animals↗

PubMed2004

Automated whole-genome multiple alignment of rat, mouse, and human.

We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment and consists of two main steps: (1) alignment of the mouse and rat genomes, and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human, and 97% of all alignments with human sequence >100 kb agree with a three-way synteny map built independently, using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment, and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

Animals↗

PubMed2004

Transforming growth factor-beta isoform expression in the perisutural tissues of craniosynostotic rabbits.

OBJECTIVE: To describe the expression patterns of the various transforming growth factor-beta (Tgf-beta) isoforms, known to be involved in suture development, in the perisutural tissues of rabbits with naturally occurring craniosynostosis and relate such differential expression to the pathogenesis of premature suture fusion. METHOD: Twenty-one coronal sutures were harvested from six wild-type control New Zealand White rabbits and five rabbits with familial coronal suture synostosis at 25 days of age for histomorphometric and immunohistochemical analyses. Tgf-beta isoform immunoreactivity was assessed using indirect immunoperoxidase procedures with specific antibodies. RESULTS: Synostosed sutures had significantly (p <.01) greater bone area and relatively more osteoblasts and osteocytes in the osteogenic fronts, compared with wild-type sutures. Tgf-beta isoform immunoreactivity showed differential staining patterns between wild-type and synostosed perisutural tissues. In wild-type sutures, Tgf-beta1 and Tgf-beta3 immunoreactivity was significantly (p <.001) greater than Tgf-beta2 staining in all perisutural tissues. In synostosed sutures, the opposite pattern was observed, with Tgf-beta2 immunoreactivity significantly (p <.001) greater than Tgf-beta1 and Tgf-beta3 in the osteogenic fronts, dura mater, and periosteum. CONCLUSIONS: Findings from this study suggest that an overexpression of Tgf-beta2, either in isolation or in association with an underexpression of Tgf-beta1 and Tgf-beta3, may be related to premature suture fusion (craniosynostosis) in this pathological rabbit model. These abnormal expression patterns may be involved in premature suture fusion either through increased cell proliferation, decreased apoptosis of the osteoblasts or both at the osteogenic fronts.

Animals↗

PubMed2003

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. We present LAGAN, a system for rapid global alignment of two homologous genomic sequences, and Multi-LAGAN, a system for multiple global alignment of genomic sequences. We tested our systems on a data set consisting of greater than 12 Mb of high-quality sequence from 12 vertebrate species. All the sequence was derived from the genomic region orthologous to an approximately 1.5-Mb region on human chromosome 7q31.3. We found that both LAGAN and Multi-LAGAN compare favorably with other leading alignment methods in correctly aligning protein-coding exons, especially between distant homologs such as human and chicken, or human and fugu. Multi-LAGAN produced the most accurate alignments, while requiring just 75 minutes on a personal computer to obtain the multiple alignment of all 12 sequences. Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu.

Animals↗

PubMed2003

Genomic regulatory regions: insights from comparative sequence analysis.

Comparative sequence analysis is contributing to the identification and characterization of genomic regulatory regions with functional roles. It is effective because functionally important regions tend to evolve at a slower rate than do less important regions. The choice of species for comparative analysis is crucial: shared ancestry of a clade of species facilitates the discovery of genomic features important to that clade, whereas increased sequence divergence improves the resolution at which features can be discovered. Recent studies suggest that comparative analyses are useful for all branches of life and that, in the near future, large-scale mammalian comparative sequence analysis will provide the best approach for the comprehensive discovery of human regulatory elements.

Animals↗

PubMed2003

Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.

Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of evolutionary constraint at the single nucleotide level. High-resolution quantification would be informative for determining the distribution of important positions within functional elements and for evaluating the relative importance of nucleotide sites that carry single nucleotide polymorphisms (SNPs). Because the level of resolution in comparative sequence analyses is a direct function of sequence diversity, we propose that the information content of a candidate mammalian genome be defined as the sequence divergence it would add relative to already-sequenced genomes. We show that reliable estimates of genomic sequence divergence can be obtained from small genomic regions. On the basis of a multiple sequence alignment of approximately 1.4 megabases each from eight mammals, we generate such estimates for five unsequenced mammals. Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses.

Animals↗

PubMed2002

Coronal suturectomy does not cause acute postoperative displacement in the cranial bases of craniosynostotic rabbits.

Approximately 300 to 500 infants per 1,000,000 have prematurely fused cranial sutures (craniosynostosis). Craniosynostosis can result in increased intracranial pressure and craniofacial deformities, which often require extensive and costly craniofacial surgery. Because the neurocranium and basicranium are developmentally interrelated, understanding their influence on one another is important for surgical planning. Although surgery has been found to have long-term effects on the cranial bases of craniosynostotic human beings and rabbits, the biological mechanisms behind these effects remain uncertain. Some researchers have suggested that the surgical release of synostosed sutures alters long-term growth patterns, resulting in cranial base differences between craniosynostotic individuals who undergo surgery and those who do not. Additionally, some investigators have proposed that an acute and surgically related displacement of basicranial elements may contribute to the observed differences. The current study examines acute postoperative changes in four lengths, three angles, and three triangles between cranial base landmarks in a sample of seven New Zealand white rabbits with familial nonsyndromic craniosynostosis. Results indicate that suturectomy caused no statistically significant (P < 0.05) acute length, angular, or shape differences in the cranial base. Thus, previous long-term cranial base differences found between rabbits that were operated on and those that were not were probably not caused by an acute displacement of skeletal elements as a result of surgery. These findings suggest that postoperative cranial base changes may be related more to chronically altered growth patterns than to acutely altered changes in intracranial pressure or dural tension.

Acute Disease↗