Biomedical subjects

James Chen

Publications and source records attributed to James Chen.

12 recordsLinked to original sources

PubMed2026

The phenotypic landscape of the mycobacterial cell.

The Mycobacteriales are an order of diverse bacteria that thrive in many environmental and host-associated niches. Because the most notorious member of this clade, Mycobacterium tuberculosis, is a major human pathogen, research on Mycobacteriales has focused on pathogenesis, and, as a consequence, many fundamental aspects of Mycobacterial biology remain understudied. Here, we address this gap by performing a genome-wide CRISPRi chemical genomics screen using a diverse set of >35 antibiotics, detergents, and other anti-microbials predominantly targeting the cell envelope of Mycobacterium smegmatis, a saprophytic model Mycobacterium. We highlight new information derived from this screen, including the identification of novel functions for previously uncharacterized conserved and essential genes (in mycolic acid and arabinogalactan synthesis), the discovery of a new drug scaffold/protein target pair, and insights into the mechanism of action of two commonly used antibiotics. These data are also a valuable resource for the mycobacterial research community, as they provide thousands of novel phenotypes for uncharacterized genes and meaningful phenotypic correlations between annotated and uncharacterized genes.

Journal Article↗

PubMed2006

Rotational angiography (RA) and three-dimensional imaging (3-DRA): an available clinical tool.

Being able to accurately choose an optimal view for stent positioning, non foreshortened length and to avoid side branches is imperative during therapeutic procedures. Traditional imaging limitations may include the selection of an incorrectly sized stent, inaccurate placement, and/or the need for additional stents. With the use of newer acquisition techniques and three-dimensional (3-D) modeling/reconstructions this can be minimized. We present a case in which with the assistance of 3-D and its computer derived optimal view, and optimal length, a significant amount of vessel foreshortening was eliminated therefore improving the procedural outcome.

Angioplasty, Balloon, Coronary↗

PubMed2006

In vitro characterization of human dental pulp cells: various isolation methods and culturing environments.

Our purpose was to characterize human dental pulp cells isolated by various methods and to examine the behavior of cells grown under various conditions for the purpose of pulp/dentin tissue engineering and regeneration. We compared the growth of human pulp cells isolated by either enzyme digestion or the outgrowth method. Expression of dentin sialophosphoprotein, Cbfa1, and two types of collagen (I and III) in these cells was examined by Western blot or reverse transcription/polymerase chain reaction. Growth of pulp cells on dentin and in collagen gel was also characterized. We found that different isolation methods give rise to different populations or lineages of pulp cells during in vitro passage based on their collagen gene expression patterns. Cells isolated by enzymedigestion had a higher proliferation rate than those isolated by outgrowth. Pulp cells did not proliferate or grew minimally on chemically and mechanically treated dentin surface and appeared to establish an odontoblast-like morphology with a cytoplasmic process extending into a dentinal tubule as revealed by scanning electron microscopy. The contraction of the collagen matrix caused by pulp cells was dramatic: down to 34% on day 14. Our data indicate that (1) the choice of the pulp cell isolation method may affect the distribution of the obtained cell populations, (2) a treated dentin surface might still promote odontoblast differentiation, and (3) a collagen matrix may not be a suitable scaffold for pulp tissue regeneration because of the marked contraction caused by pulp cells in the matrix. The present study thus provides important information and a basis for further investigations pre-requisite to establishing pulp tissue engineering/regeneration protocols.

Base Sequence↗

PubMed2006

Primary glioblastomas express mesenchymal stem-like properties.

Glioblastoma is the most common and aggressive primary brain cancer. Recent isolation and characterization of brain tumor-initiating cells supports the concept that transformed neural stem cells may seed glioblastoma. We previously identified a wide array of mesenchymal tissue transcripts overexpressed in a broad set of primary glioblastoma (de novo) tumors but not in secondary glioblastoma (derived from lower-grade) tumors, low-grade astrocytomas, or normal brain tissues. Here, we extend this observation and show that a subset of primary glioblastoma tumors and their derived tumor lines express cellular and molecular markers that are associated with mesenchymal stem cells (MSC) and that glioblastoma cell cultures can be induced to differentiate into multiple mesenchymal lineage-like cell types. These findings suggest either that a subset of primary glioblastomas derive from transformed stem cells containing MSC-like properties and retain partial phenotypic aspects of a MSC nature in tumors or that glioblastomas activate a series of genes that result in mesenchymal properties of the cancer cells to effect sustained tumor growth and malignant progression.

Antigens, Surface↗

PubMed2004

Building an organ-specific carcinogenic database for SAR analyses.

FDA reviewers need a means to rapidly predict organ-specific carcinogenicity to aid in evaluating new chemicals submitted for approval. This research addressed the building of a database to use in developing a predictive model for such an application based on structure-activity relationships (SAR). The Internet availability of the Carcinogenic Potency Database (CPDB) provided a solid foundation on which to base such a model. The addition of molecular structures to the CPDB provided the extra ingredient necessary for SAR analyses. However, the CPDB had to be compressed from a multirecord to a single record per chemical database; multiple records representing each gender, species, route of administration, and organ-specific toxicity had to be summarized into a single record for each study. Multiple studies on a single chemical had to be further reduced based on a hierarchical scheme. Structural cleanup involved removal of all chemicals that would impede the accurate generation of SAR type descriptors from commercial software programs; that is, inorganic chemicals, mixtures, and organometallics were removed. Counterions such as Na, K, sulfates, hydrates, and salts were also removed for structural consistency. Structural modification sometimes resulted in duplicate records that also had to be reduced to a single record based on the hierarchical scheme. The modified database containing 999 chemicals was evaluated for liver-specific carcinogenicity using a variety of analysis techniques. These preliminary analyses all yielded approximately the same results with an overall predictability of about 63%, which was comprised of a sensitivity of about 30% and a specificity of about 77%.

Animals↗

PubMed2004

Budget negotiation for industry-sponsored clinical trials.

The specialty of anesthesia is well suited to attract industry-sponsored clinical trials and research revenues because of its fundamental contributions to surgery, critical care, and pain medicine. However, the performance and budgeting of industry-sponsored clinical research over the past decade has been significantly altered by the rapid growth of commercially oriented networks of contract-research organizations and site-management organizations. Further, the competitive nature of today's clinical research climate can make the planning and negotiating of study budgets and contracts stressful, time consuming, frustrating, and full of pitfalls. Because a clinical trial contract is a fixed-price agreement, investigators are obligated to perform the work described in the contract, even if the actual costs exceed the study contract. Successful budgeting for the performance of an industry-sponsored clinical trial thus requires a thorough understanding of the direct and indirect costs associated with performing clinical research. We reviewed budget and contractual considerations for the successful negotiation and performance of industry-sponsored clinical research.

Budgets↗

PubMed2003

Electron cryomicroscopy structure of N-ethyl maleimide sensitive factor at 11 A resolution.

N-ethyl maleimide sensitive factor (NSF) belongs to the AAA family of ATPases and is involved in a number of cellular functions, including vesicle fusion and trafficking of membrane proteins. We present the three-dimensional structure of the hydrolysis mutant E329Q of NSF complexed with an ATP-ADP mixture at 11 A resolution by electron cryomicroscopy and single-particle averaging of NSF.alpha-SNAP.SNARE complexes. The NSF domains D1 and D2 form hexameric rings that are arranged in a double-layered barrel. Our structure is more consistent with an antiparallel orientation of the two rings rather than a parallel one. The crystal structure of the D2 domain of NSF was docked into the EM density map and shows good agreement, including details at the secondary structural level. Six protrusions corresponding to the N domain of NSF (NSF-N) emerge from the sides of the D1 domain ring. The density corresponding to alpha-SNAP and SNAREs is located on the 6-fold axis of the structure, near the NSF-N domains. The density of the N domain is weak, suggesting conformational variability in this part of NSF.

Adenosine Triphosphatases↗

PubMed2003

hMad4, c-Myc endogenous inhibitor, induces a replicative senescence-like state when overexpressed in human fibroblasts.

Mad family proteins have an antagonistic action on Myc-dependent cell proliferation and transformation. We isolated a human cDNA clone, human Mad4 (hMad4), encoding a polypeptide of 209 amino acid residues, exhibiting 90% identity with mouse Mad4. Northern blot analysis shows that hMad4 probe hybridizes to a 3.8 kb message; its expression is highest in quiescent human WI38 fibroblasts. Among tissues, hMad4 mRNA is most abundant in brain, lung, and muscle. Consistent with other members of the Mad family, hMad4 can repress the transactivation activity of Myc/Max heterodimers on an E-box chloramphenicol acteyl transferase (CAT) reporter plasmid; inhibition of both proliferation and clonogenic formation of hMad4-infected cells correlates with the in vitro reporter repression. Moreover, infection of young human fibroblasts induces a replicative senescence-like state. This phenotype was accompanied by s-beta-galactosidase and PAI-1 expression. These results suggest that hMad4 might be an important regulator of replicative senescence in human cells.

Amino Acid Sequence↗

PubMed2002

Impact of mobility on structure-based drug design for the MMPs.

Structure-based approaches for drug design generally do not incorporate solvent effects and dynamic information to predict inhibitor-binding affinity because of practical limitations. The matrix metalloproteinases (MMPs) have previously been demonstrated to exhibit significant mobility in their active sites. This dynamic characteristic significantly complicates the drug design process based on static structures, which was clearly observed for a class of hydroxamic acids containing a butynyl moiety. Compound 1 was expected to be selective against MMP-1 based on predicted steric clashes between the butynyl P1' group and the S1' pocket, but the observation of complex inhibitor dynamics in the NMR structure of MMP-1:1 provides an explanation for the low nanomolar binding to MMP-1.

Binding Sites↗

PubMed2002

The checkpoint protein Chfr is a ligase that ubiquitinates Plk1 and inhibits Cdc2 at the G2 to M transition.

The checkpoint protein Chfr delays entry into mitosis, in the presence of mitotic stress (Scolnick, D.M., and T.D. Halazonetis. 2000. Nature. 406:430-435). We show here that Chfr is a ubiquitin ligase, both in vitro and in vivo. When transfected into HEK293T cells, Myc-Chfr promotes the formation of high molecular weight ubiquitin conjugates. The ring finger domain in Chfr is required for the ligase activity; this domain auto-ubiquitinates, and mutations of conserved residues in this domain abolish the ligase activity. Using Xenopus cell-free extracts, we demonstrated that Chfr delays the entry into mitosis by negatively regulating the activation of the Cdc2 kinase at the G2-M transition. Specifically, the Chfr pathway prolongs the phosphorylated state of tyrosine 15 in Cdc2. The Chfr-mediated cell cycle delay requires ubiquitin-dependent protein degradation, because inactivating mutations in Chfr, interference with poly-ubiquitination, and inhibition of proteasomes all abolish this delay in mitotic entry. The direct target of the Chfr pathway is Polo-like kinase 1 (Plk1). Ubiquitination of Plk1 by Chfr delays the activation of the Cdc25C phosphatase and the inactivation of the Wee1 kinase, leading to a delay in Cdc2 activation. Thus, the Chfr pathway represents a novel checkpoint pathway that regulates the entry into mitosis by ubiquitin-dependent proteolysis.

Animals↗

PubMed2002

The effects of the introduction of a high-nutrient transitional formula on growth and development of very-low-birth-weight infants.

OBJECTIVE: The purpose of this study was to determine the impact of introducing a high-nutrient transitional formula (TF) for use after discharge on the growth and development of premature infants. STUDY DESIGN AND METHODS: This was a cohort study of all surviving infants with a birth weight < or =1250 g admitted to the neonatal intensive care unit between January 1, 1995 and December 31, 1996. Infants with major congenital abnormalities were excluded. There were 180 infants discharged, including 66 on TF and 114 on standard formulas for full-term infants. RESULTS: Use of TF started the week before discharge, and increased from 10% in 1995 to 66% in 1996 (p<0.001). Regression analyses controlling for multiple confounders identified TF as a significant contributor to improved weight at 3 months and length at 18 months. Bayley developmental scores were not affected. CONCLUSION: Introduction of a TF for very-low-birth-weight infants resulted in improved growth after discharge.

Anthropometry↗

PubMedDate not supplied

New technology for deep light distribution in tissue for phototherapy.

Photodynamic therapy is one of several techniques developed for phototherapy for solid cancers and hematologic malignancies. Photodynamic therapy is a treatment that utilizes a molecular energy exchange between visible light and a photosensitive drug, which results in the production of 1O2, a highly reactive cytocidal oxygen species. The effect is limited to the region where light and drug are combined so that malignant tissue is destroyed and the usual side effects associated with standard cancer therapies are avoided. The light component of photodynamic therapy is customarily generated via dye-pumped or diode lasers. The cost and the complexity of lasers have seriously limited the clinical use of photodynamic therapy for malignancies. A new device technology, based on light-emitting diodes, has been developed (Light Sciences Corporation, Issaquah, WA) that allows light production inside the target tissue. This new technology will expand the current range of indications that are treatable with photodynamic therapy to include moderate- and large-volume refractorytumors. Conventional photodynamic therapy utilizes the delivery of intense light for seconds or minutes. The new approach differs from conventional photodynamic therapy in that it combines a novel interstitial light delivery system with prolonged photoactivation of photosensitive drugs. Prolonging photoactivation time in order to deliver a higher light dose results in an amplification effect, whereby the repeated activation of each photosensitive drug molecule leads to the generation of many thousands of 1O2 molecules. The production of overwhelming numbers of these powerful oxidants in individual cells and the vascular supply of tumors leads to irreversible damage and death of the targeted lesions. Results of preclinical studies have indicated a significant correlation between increased duration of photoactivation and increased volume and depth of photodynamic therapy-induced necrosis. The new developments will enable photodynamic therapy to be used effectively against refractory bulky disease as frontline therapy or in combination with chemotherapy, radiation therapy, or biologics. Perhaps most promising, many patients with advanced refractory disease may now be relieved of symptoms or may return to the treatable population.

Animals↗