Identification of G1-Regulated Genes in Normally Cycling Human Cells

BACKGROUND: Obtaining synchronous cell populations is essential for cell-cycle studies. Methods such as serum withdrawal or use of drugs which block cells at specific points in the cell cycle alter cellular events upon re-entry into the cell cycle. Regulatory events occurring in early G1 phase of a new cell cycle could have been overlooked. METHODOLOGY AND FINDINGS: We used a robotic mitotic shake-off apparatus to select cells in late mitosis for genome-wide gene expression studies. Two separate microarray experiments were conducted, one which involved isolation of RNA hourly for several hours from synchronous cell populations, and one experiment which examined gene activity every 15 minutes from late telophase of mitosis into G1 phase. To verify synchrony of the cell populations under study, we utilized methods including BrdU uptake, FACS, and microarray analyses of histone gene activity. We also examined stress response gene activity. Our analysis enabled identification of 200 early G1-regulated genes, many of which currently have unknown functions. We also confirmed the expression of a set of genes candidates (fos, atf3 and tceb) by qPCR to further validate the newly identified genes. CONCLUSION AND SIGNIFICANCE: Genome-scale expression analyses of the first two hours of G1 in naturally cycling cells enabled the discovery of a unique set of G1-regulated genes, many of which currently have unknown functions, in cells progressing normally through the cell division cycle. This group of genes may contain future targets for drug development and treatment of human disease

Systematic quantification of gene interactions by phenotypic array analysis

A phenotypic array method, developed for quantifying cell growth, was applied to the haploid and homozygous diploid yeast deletion strain sets. A growth index was developed to screen for non-additive interacting effects between gene deletion and induced perturbations. From a genome screen for hydroxyurea (HU) chemical-genetic interactions, 298 haploid deletion strains were selected for further analysis. The strength of interactions was quantified using a wide range of HU concentrations affecting reference strain growth. The selectivity of interaction was determined by comparison with drugs targeting other cellular processes. Bio-modules were defined as gene clusters with shared strength and selectivity of interaction profiles. The functions and connectivity of modules involved in processes such as DNA repair, protein secretion and metabolic control were inferred from their respective gene composition. The work provides an example of, and a general experimental framework for, quantitative analysis of gene interaction networks that buffer cell growth

Antineoplastic Drugs as a Potential Risk Factor in Occupational Settings: Mechanisms of Action at the Cell Level, Genotoxic Effects, and Their Detection Using Different Biomarkers

U članku je prikazana osnovna podjela antineoplastičnih lijekova prema mehanizmima djelovanja na razini stanice. Objašnjeni su mehanizmi genotoksičnosti najvažnijih vrsta lijekova koji se primjenjuju u okviru uobičajenih protokola za liječenje zloćudnih novotvorina. Navedena je važeća klasifi kacija antineoplastika prema kancerogenom potencijalu, podaci o mutagenom potencijalu te je prikazana njihova podjela u skladu s anatomsko-terapijsko-kemijskim sustavom klasifi kacije. Sustavno su prikazani najvažniji rezultati svjetskih i hrvatskih istraživanja na populacijama radnika izloženih antineoplasticima, provedenih u razdoblju 1980.-2009. s pomoću četiri najčešće primjenjivane metode: analize izmjena sestrinskih kromatida, analize kromosomskih aberacija, mikronukleus-testa i komet-testa. Objašnjena su osnovna načela navedenih metoda te raspravljene njihove prednosti i nedostaci. Biološki pokazatelji daju važne podatke o individualnoj osjetljivosti profesionalno izloženih ispitanika koji mogu poslužiti unaprjeđenju postojećih uvjeta rada i upravljanju rizicima pri izloženosti genotoksičnim agensima. Na osnovi prednosti i nedostataka citogenetičkih metoda zaključeno je da je mikronukleus-test, koji podjednako uspješno dokazuje klastogene i aneugene učinke, jedna od najboljih metoda dostupnih za otkrivanje štetnih djelovanja antineoplastičnih lijekova koji su u aktivnoj primjeni.This article brings an overview of the mechanisms of action of antineoplastic drugs used in the clinical setting. It also describes the genotoxic potentials of the most important classes of antineoplastic drugs involved in standard chemotherapy protocols. Classifi cation of antineoplastic drugs according to the IARC monographs on the evaluation of carcinogenic risks to humans is accompanied by data on their mutagenicity and the most recent updates in the Anatomical Therapeutic Chemical (ATC) Classifi cation System. We report the main fi ndings of biomonitoring studies that were conducted in exposed healthcare workers all over the world between 1980 and 2009 using four biomarkers: sister chromatid exchanges, chromosome aberrations, micronuclei. and the comet assay. The methods are briefl y explained and their advantages and disadvantages discussed. Biomarkers provide important information on individual genome sensitivity, which eventually might help to improve current working practices and to manage the risks related with exposure to genotoxic agents. Taking into consideration all known advantages and drawbacks of the existing cytogenetic methods, the micronucleus assay, which is able to detect both clastogenic and aneugenic action, is the most suitable biomarker for assessing harmful effects of antineoplastic drugs currently used in health care

TRANSFER OF EXCESS NUCLEAR MATERIAL FROM LOS ALAMOS TO SAVANNAH RIVER SITE FOR LONG-TERM DISPOSITION

Los Alamos National Laboratory is preparing excess nuclear material for shipment to Savannah River Site (SRS) for final disposition. Prior to shipment the nuclear material will be stabilized and packaged to meet strict criteria. The criterion that must be met include: (1) the DOE stabilization, packaging and storage requirements for plutonium bearing materials, DOE-STD-3013, (2) shipping container packaging requirements, (3) SRS packaging and storage criteria, and (4) DOE Material Disposition criteria for either immobilization or MOX reactor fuel. Another issue in preparing for this transfer is the DOE certification of shipping containers and the availability of shipping containers. This transfer of the nuclear material is fully supported by the EM, DP and NN Sections of the DOE, as well as, by LANL and SRS, yet a strong collaboration is needed to meet all established requirements relating to stabilization, packaging, shipment, storage and final disposition. This paper will present the overall objectives, the issues and the planned strategy to accomplish this nuclear material transfer

Facility Model for the Los Alamos Plutonium Facility

The Los Alamos Plutonium Facility contains more than sixty unit processes and handles a large variety of nuclear materials, including many forms of plutonium-bearing scrap. The management of the Plutonium Facility is supporting the development of a computer model of the facility as a means of effectively integrating the large amount of information required for material control, process planning, and facility development. The model is designed to provide a flexible, easily maintainable facility description that allows the faciltiy to be represented at any desired level of detail within a single modeling framework, and to do this using a model program and data files that can be read and understood by a technically qualified person without modeling experience. These characteristics were achieved by structuring the model so that all facility data is contained in data files, formulating the model in a simulation language that provides a flexible set of data structures and permits a near-English-language syntax, and using a description for unit processes that can represent either a true unit process or a major subsection of the facility. Use of the model is illustrated by applying it to two configurations of a fictitious nuclear material processing line

Inventory planning for feed metal production and excess materials disposition.

Inventory planning and scheduling at the Los Alamos National Laboratory nuclear facility (TA-55) has become increasingly demanding given the limited supply of nuclear materials available for weapons production. This limitation comes from the shutdown of nuclear production reactors as well as the declaration of materials excess to national security within the DOE complex. The materials that have been declared excess to national security cannot be used in support of nuclear weapons activities and must be appropriately dispositioned. The matrices of the excess materials and the materials in the weapons; stream are often similar, if not identical, and must be processed and/or packaged utilizing the same personnel and facility resources. In order to segregate these materials and continue weapons production and dispositioning operations concurrently, careful tracking at the item level is required. Scheduling and campaigning of these materials must also be carefully monitored in order to meet both nuclear weapons production schedules as well as dispositioning milestones. All planning activities must consider the impact of processing operations on severely constrained resources including the special nuclear materials storage vault, the nondestructive assay laboratory, and the waste management and shipping operations. This paper details the methodologies and the use of simulation and other computerized tools by the Nuclear Materials Technology Division materials management organization at TA-55. These tools assist in predicting materials and resource availability and optimizing the inventory planning activities

Prognostic factors in prostate cancer. College of American Pathologists Consensus Statement 1999

Under the auspices of the College of American Pathologists, a multidisciplinary group of clinicians, pathologists, and statisticians considered prognostic and predictive factors in prostate cancer and stratified them into categories reflecting the strength of published evidence and taking into account the expert opinions of the Prostate Working Group members. Factors were ranked according to the previous College of American Pathologists categorical rankings: category I, factors proven to be of prognostic importance and useful in clinical patient management; category II, factors that have been extensively studied biologically and clinically but whose importance remains to be validated in statistically robust studies; and category III, all other factors not sufficiently studied to demonstrate their prognostic value. Factors in categories I and II were considered with respect to variations in methods of analysis, interpretation of findings, reporting of data, and statistical evaluation. For each factor, detailed recommendations for improvement were made. Recommendations were based on the following aims: (1) increasing uniformity and completeness of pathologic evaluation of tumor specimens, (2) enhancing the quality of data collected pertaining to existing prognostic factors, and (3) improving patient care. Factors ranked in category I included preoperative serum prostate-specific antigen level, TNM stage grouping, histologic grade as Gleason score, and surgical margin status. Category II factors included tumor volume, histologic type, and DNA ploidy. Factors in category III included perineural invasion, neuroendocrine differentiation, microvessel density, nuclear roundness, chromatin texture, other karyometric factors, proliferation markers, prostate-specific antigen derivatives, and other factors (oncogenes, tumor suppressor genes, apoptosis genes, etc)