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Microarray analysis of stem cells and differentiation.

Microarrays have revolutionized molecular biology and enabled biologists to perform global analysis on the expression of tens of thousands of genes simultaneously. They have been widely used in gene discovery, biomarker determination, disease classification, and studies of gene regulation. Microarrays have been applied in stem cell research to identify major features or expression signatures that define stem cells and characterize their differentiation programs toward specific lineages. Here we provide a review of the microarray technology, including the introduction of array platforms, experimental designs, RNA isolation and amplification, array hybridization, and data analysis. We also detail examples that apply microarray technology to address several of the main questions in stem cell biology.

Animals↗

Dual-Matrix Platform for Highly Specific Multi-Omics Profiling of Renal Cell Carcinoma.

Multiomics interrogation provides complementary information beyond single-omics approaches for improved disease characterization. To enable such multilayer profiling, we expanded the rapid functionalized mesoporous nanoparticle-coupled laser desorption/ionization mass spectrometry (fMNPLDI-MS) platform by designing two structurally homologous but functionally tailored fMNPs. This design enables efficient acquisition of both serum metabolic and peptide fingerprints from a total of only 2.05 μL of serum, with an LDI MS analysis time of approximately 90 s per sample, while addressing the limitation of single-matrix systems in simultaneously optimizing analytical performance for different biomolecular species. Through statistical analysis and machine learning-based feature selection, an integrated multiomics biomarker panel was established, comprising 5 peptides and 4 metabolites. Notably, this integrated panel outperformed both single-omics panels across all evaluation metrics in the validation set, improving the area under curve from 0.985 to 1.000 and increasing the classification accuracy from 0.947 (metabolites) and 0.930 (peptides) to 0.965, while showing consistent improvements in F1-score, precision, and recall. Collectively, these results demonstrate the robust performance of the dual-matrix design and multiomics integration for renal cell carcinoma classification, with potential relevance for broader applications in complex disease profiling.

Carcinoma, Renal Cell↗

Folding a nonbiological polymer into a compact multihelical structure.

The only molecules that are currently known to fold into unique three-dimensional conformations and perform sophisticated functions are biological polymers - proteins and some RNA molecules. Our aim is to create a nonbiological sequence-specific polymer that folds in aqueous solution. Toward that end, we synthesized sequence-specific 30mer, 45mer, and 60mer peptoid oligomers (N-substituted glycine polymers) consisting of 15mer units we chained together by disulfide and oxime linkages to mimic the helical bundle structures commonly found in proteins. Because these 15mer sequences were previously shown to form defined helical structures that aggregate together at submillimolar concentrations, we expected that by covalently linking multiple 15mers together, they might fold as helical bundles. To probe whether they folded, we used fluorescence resonance energy transfer (FRET) reporter groups. We found that certain constructs fold up with a hydrophobic core and have cooperative folding transitions. Such molecules may ultimately provide a platform for designing specific functions resembling those of proteins.

Chromatography, High Pressure Liquid↗

Controlled gastric emptying. 1. Effects of physical properties on gastric residence times of nondisintegrating geometric shapes in beagle dogs.

The importance of three physical parameters (size, shape, and flexibility) on gastric retention in fasting dogs was examined to assess the feasibility of designing a dosage form to achieve a consistent and predictable residence in the stomach. Test shapes were molded from Silastic elastomer or made from extruded polyethylene or polyethylene blends and included 15% barium sulfate for X-ray visualization. Beagle dogs were dosed with test shapes administered in gelatin capsules. Gastric retention was monitored by X ray over a 24-hr period. Six shapes (ring, tetrahedron, cloverleaf, disk, string, and pellet) were screened in vivo for their gastric retention potential. The tetrahedrons (each leg 2 cm in length) exhibited 91-100% retention at 24 hr. The rings (3.6-cm diameter) provided 100% retention at 24 hr. Rings and tetrahedrons of varying flexural moduli were prepared by blending low-density polyethylene and ethylene:vinyl acetate copolymer. A positive correlation existed between flexural modulus and gastric retention. The results indicate that it is feasible to design a platform for a dosage form that can be administered to beagle dogs in capsule form and be retained for 24 hr.

Animals↗

Establishing a national pediatric stem cell transplantation registry in Iran addressing implementation and data quality challenges.

The Iranian Pediatric Hematopoietic Stem Cell Transplantation Registry (IPED-HSCT) was established to enhance data collection, improve patient outcomes, and support clinical research in pediatric hematopoietic stem cell transplantation. This study aimed to assess the feasibility and reliability of implementing a standardized registry in pediatric settings. A community-based participatory study was conducted across three pediatric HSCT centers in Iran. The registry development involved a multi-phase approach, including pilot testing and the implementation of a web-based system. Data were collected from fifty pediatric patients who underwent HSCT for both malignant and non-malignant conditions, with a focus on data completeness and user satisfaction. Statistical analyses were performed using IBM SPSS Statistics. The registry achieved a data completeness rate exceeding 90%, with a participant demographic of 31 males (62%) and 19 females (38%). Rigorous quality control measures and real-time validation rules were implemented, enhancing data reliability. User feedback indicated high satisfaction with the platform's design and training sessions. Challenges included variations in long-term follow-up data collection across centers. The IPED-HSCT Registry demonstrates that establishing a robust pediatric HSCT registry is feasible even in resource-limited settings. Its innovative features offer a scalable model for similar initiatives in developing countries. Future research should focus on ensuring long-term sustainability and fostering international collaborations to improve pediatric HSCT outcomes globally. not applicable.

Humans↗

Simultaneous measurement of back and front foot ground reaction forces during the same delivery stride of the fast-medium bowler.

Six male cricket bowlers (mean +/- s(mean): age 23.5 +/- 1.3 years; height 1.83 +/- 0.04 m; body weight 826 +/- 20 N) performed their typical bowling action at a set of stumps positioned at standard pitch length (20.1 m). A specially designed force platform rig allowed the correct positioning of two force platforms to be achieved beneath an outdoor polyflex runway (0.017 m depth) for each player's delivery stride pattern. For the back foot, the peak vertical ground reaction force was 1.95 +/- 0.08 kN (2.37 +/- 0.14 BW) and the braking force was 0.77 +/- 0.12 kN (0.94 +/- 0.16 BW). For the front foot, the peak vertical force was 4.80 +/- 0.92 kN (5.75 +/- 0.98 BW) and the braking force was 2.93 +/- 0.56 kN (3.54 +/- 0.67 BW). The mean peak vertical loading rate for front foot contact was 205 +/- 52.8 kN x s(-1) (249 +/- 64 BW x s(-1)) with mean values ranging from 81 to 446 kN x s(-1) (98 to 540 BW x s(-1)). The range for back foot contact was much smaller, 25-70 kN x s(-1) (30-85 BW x s(-1)), with a mean of 41.7 +/- 7.10 kN x s(-1) (50.6 +/- 8.6 BW x s(-1)). Mean peak impact occurred 24 ms after touchdown for the back foot and 16 ms after touchdown for the front foot. At impact, mean peak loading rates were greater for the front foot at 246 kN x s(-1) (298 BW x s(-1)), with a range of 80-483 kN x s(-1) (98-534 BW x s(-1)), than for the back foot at 65 kN x s(-1) (79 BW x s(-1)), with a range of 40-84 kN x s(-1) (49-110 BW x s(-1)).

Adult↗

Standards and guidelines for CFTR mutation testing.

One mission of the ACMG Laboratory Quality Assurance (QA) Committee is to develop standards and guidelines for clinical genetics laboratories, including cytogenetics, biochemical, and molecular genetics specialties. This document was developed under the auspices of the Molecular Subcommittee of the Laboratory QA Committee by the Cystic Fibrosis (CF) Working Group. It was placed on the "fast track" to address the preanalytical, analytical, and postanalytical quality assurance practices of laboratories currently providing testing for CF. Due to the anticipated impact of the ACMG recommendation statement endorsing carrier testing of reproductive couples, it was viewed that CF testing would increase in volume and that the number of laboratories offering CF testing would also likely increase. Therefore, this document was drafted with the premise of providing useful information gained by experienced laboratory directors who have provided such testing for many years. In many instances, "tips" are given. However, these guidelines are not to be interpreted as restrictive or the only approach but to provide a helpful guide. Certainly, appropriately trained and credentialed laboratory directors have flexibility to utilize various testing platforms and design testing strategies with considerable latitude. We felt that it was essential to include technique-specific guidelines of several current technologies commonly used in laboratories providing CF testing, since three of the four technologies discussed are available commercially and are widely utilized. We take the view that these technologies will change, and thus this document will change with future review.

Cystic Fibrosis↗

Technical standards and guidelines for Huntington disease testing.

One mission of the ACMG Laboratory Quality Assurance (QA) Committee is to develop standards and guidelines for clinical genetics laboratories, including cytogenetics, biochemical, and molecular genetics specialties. This document was developed under the auspices of the Molecular Subcommittee of the Laboratory QA Committee by the Huntington Disease (HD) Working Group. These guidelines are not to be interpreted as restrictive or the only approach but to provide a helpful guide. Certainly, appropriately trained and credentialed laboratory directors have flexibility to utilize various testing platforms and design testing strategies with considerable latitude. We felt that it was essential to include technique-specific guidelines of several current technologies commonly used in laboratories providing HD testing, because the technologies discussed are available commercially and are widely utilized. We take the view that these technologies may change, and thus this document may change with future review.

Credentialing↗

Effect of liquid and paste-type lubricants on torque values during simulated rotary root canal instrumentation.

AIM: To evaluate the effects of lubrication on torque generated during rotary preparation of simulated root canals in dentine using ProFile and ProTaper Nickel-Titanium instruments. METHODOLOGY: Thirty-two 3 mm thick dentine discs were used for this study. Four pilot holes were drilled perpendicularly through each disc. These simulated root canals were filled with water, aqueous 15% ethylenediamine tetraacetic acid (EDTA) or a paste-type lubricant (Glyde). Empty canals served as controls. Peak torque values and apically directed forces of rotary instruments were measured using a specially designed testing platform. Full torsional loads over time were calculated by integration of continuous torque records. Data were compared using analyses of variance with the alpha-type error set at 0.05. RESULTS: Maximum torque values using ProFile instruments were significantly (P < 0.005) reduced by the EDTA solution, whilst no reduction was observed using Glyde. With ProTaper instruments, no lubricant effects on maximum torque values were observed (P = 0.372). Full torsional loads over time were significantly reduced for both ProFile and ProTaper preparation (P < 0.005) by the use of lubrication. The two fluids performed significantly better than paste-based Glyde. All lubricants reduced force when applied to ProTaper by mean reductions ranging from 12 to 54%, whilst Glyde lead to increased force when applied to ProFile. CONCLUSIONS: Under the conditions of this laboratory study, lubrication appeared to be advantageous. Aqueous solutions generally performed better than the paste-type product under investigation, which showed untoward effects when used in conjunction with a rotary instrument with a U-shaped cross-section (ProFile).

Analysis of Variance↗

Peroxisome proliferator-activated receptor gamma-independent repression of prostate-specific antigen expression by thiazolidinediones in prostate cancer cells.

In light of the potential use of the thiazolidinedione family of peroxisome proliferator-activated receptor-gamma (PPARgamma) agonists in prostate cancer treatment, this study assessed the mechanism by which these agents suppress prostate-specific antigen (PSA) secretion in prostate cancer cells. Two lines of evidence indicate that the effect of thiazolidinediones on PSA down-regulation is independent of PPARgamma activation. First, this thiazolidinedione-mediated PSA down-regulation is structure-specific irrespective of the relative PPARgamma agonist potency. Second, the PPARgamma-inactive analogs of troglitazone and ciglitazone [Delta2TG (5-[4-(6-hydroxy-2,5,7,8-tetramethyl-chroman-2-yl-methoxy)-benzylidene]-thiazolidine-2,4-dione) and Delta2CG (5-[4-(1-methyl-cyclohexylmethoxy)-benzylidene]-thiazolidine-2,4-dione), respectively] exhibit higher potency than the parent compound in inhibiting dihydrotestosterone (DHT)-stimulated PSA secretion. Although 10 microM troglitazone and Delta2TG significantly inhibit PSA secretion, they do not alter the expression level of androgen receptor (AR) or interfere with DHT-activated nuclear translocation of AR. However, reporter gene and chromatin immunoprecipitation studies indicate that troglitazone and Delta2TG block AR recruitment to the androgen response elements within the PSA promoter. Thus, this study raises the question of whether the ability of oral troglitazone to reduce PSA levels in prostate cancer patients is therapeutically relevant. A major concern is that the concentration for troglitazone to mediate antitumor effects is severalfold higher than that of PSA down-regulation, which is difficult to attain at therapeutic doses. Nevertheless, it is noteworthy that troglitazone and Delta2TG at high doses were able to inhibit AR expression. From a translational perspective, separation of PPARgamma agonist activity from AR down-regulation provides a molecular basis to use troglitazone as a platform to design AR-ablative agents.

Animals↗

BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging.

The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.

Algorithms↗

A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling.

Physiological, morphological, and transcriptional alterations elicited by ethynyl estradiol in the uteri of Sprague-Dawley rats and C57BL/6 mice were assessed using comparable study designs, microarray platforms, and analysis methods to identify conserved estrogen signaling networks. Comparative analysis identified 153 orthologous gene pairs that were positively correlated, suggesting conserved transcriptional targets important in uterine proliferation. Functional annotation for these responses were associated with angiogenesis, water and solute transport, cell cycle control, redox control, DNA replication, protein synthesis and transport, xenobiotic metabolism, cell-cell communication, energetics, and cholesterol and fatty acid regulation. The identification of conserved temporal expression patterns of these orthologs provides experimental support for the transfer of functional annotation from mouse orthologs to 44 previously unannotated rat expressed sequence tags based on their homology and co-expression patterns. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates the ability of systematic comparative genomic assessments to elucidate important conserved mechanisms in rodent estrogen signaling during uterine proliferation.

Animals↗

Patterns and prevalence of arrest in a statewide cohort of mental health care consumers.

OBJECTIVE: Although criminal justice involvement among persons with severe mental illness is a much discussed topic, few large-scale studies systematically describe the patterns and prevalence of arrest in this population. This study examined rates, patterns, offenses, and sociodemographic correlates of arrest in a large cohort of mental health service recipients. METHODS: The arrest records of 13,816 individuals receiving services from the Massachusetts Department of Mental Health from 1991 to 1992 were examined over roughly a ten-year period. Bivariate relationships between sociodemographic factors and arrest were also examined. RESULTS: About 28 percent of the cohort experienced at least one arrest. The most common charges were crimes against public order followed by serious violent offenses and minor property crime. The number of arrests per individual ranged from one to 71. Five percent of arrestees (roughly 1.5 percent of the cohort) accounted for roughly 17 percent of arrests. The proportion of men arrested was double that of women. Persons 18 to 25 years of age had a 50 percent chance of at least one arrest. This rate declined with age but did so unevenly across offense types. CONCLUSIONS: The likelihood of arrest appeared substantial among persons with severe mental illness, but the bulk of offending appeared concentrated in a small group of persons and among persons with sociodemographic features similar to those of offenders in the general population. Data such as these could provide a platform for designing jail diversion and other services to reduce both initial and repeat offending among persons with serious mental illness.

Adolescent↗

Global down-regulation of HOX gene expression in PML-RARalpha + acute promyelocytic leukemia identified by small-array real-time PCR.

Acute promyelocytic leukemia (APL) is associated with a reciprocal and balanced translocation involving the retinoic acid receptor-alpha (RARalpha). All-trans retinoic acid (ATRA) is used to treat APL and is a potent morphogen that regulates HOX gene expression in embryogenesis and organogenesis. HOX genes are also involved in hematopoiesis and leukemogenesis. Thirty-nine mammalian HOX genes have been identified and classified into 13 paralogous groups clustered on 4 chromosomes. They encode a complex network of transcription regulatory proteins whose precise targets remain poorly understood. The overall function of the network appears to be dictated by gene dosage. To investigate the mechanisms involved in HOX gene regulation in hematopoiesis and leukemogenesis by precise measurement of individual HOX genes, a small-array real-time HOX (SMART-HOX) quantitative polymerase chain reaction (PCR) platform was designed and validated. Application of SMART-HOX to 16 APL bone marrow samples revealed a global down-regulation of 26 HOX genes compared with normal controls. HOX gene expression was also altered during differentiation induced by ATRA in the PML-RARalpha(+) NB4 cell line. PML-RARalpha fusion proteins have been reported to act as part of a repressor complex during myeloid cell differentiation, and a model linking HOX gene expression to this PML-RARalpha repressor complex is now proposed.

Bone Marrow↗

Geographic variation in thermal sensitivity of jumping performance in the frog Limnodynastes peronii.

I compared the thermal sensitivity of jumping performance of five populations of the striped marsh frog (Limnodynastes peronii) over a wide geographic range extending from the cool-temperate south to the tropical north of Australia. Maximum jumping performance of adult L. peronii was assessed for each population at eight temperatures between 5 degrees C and 32 degrees C using a custom-designed force platform. From force recordings for each individual jump, maximum jumping force (F(max)) and acceleration (A(max)) and maximum power output (P(max)), take-off velocity (U(max)), jump distance (D(J)) and contact time on the platform (T(C)) were calculated. The body mass of adult L. peronii varied over their geographic range, from approximately 5 g for the lowland tropical population to more than 22 g for the cool-temperate populations. The thermal sensitivity of jumping performance varied over their geographic range, with the populations from the cooler climates generally performing better than those from the warmer climate populations at the cooler temperatures, and vice versa at the higher temperatures. However, not all parameters of jumping performance underwent parallel changes in thermal sensitivity amongst the populations of L. peronii. Only minor differences in the shape of the thermal sensitivity curves for F(max) and A(max) were detected amongst the populations, while the thermal sensitivities of U(max), D(J) and P(max) all displayed considerable variation amongst the populations. The optimal temperatures for U(max), D(J) and P(max) were generally lower in the cool-temperate populations than in the tropical populations of L. peronii. To determine whether this geographic variation was due to genetic variation, or merely reflected phenotypic plasticity, I also compared the thermal sensitivity of jumping performance between metamorph L. peronii from two different populations raised under identical conditions in the laboratory. The maximum jumping distance of the metamorph L. peronii was assessed at seven temperatures between 8 degress C and 35 degrees C for the two latitudinally extreme populations (i.e. lowland tropical Proserpine and cool-temperate Gippsland populations). Like adult L. peronii, the metamorphs from the cool-temperate population jumped further than those from the lowland tropical population at the lower temperatures, although no differences were detected at the higher temperatures. Thus, geographic variation in thermal sensitivity of jumping performance in L. peronii probably has a genetic component, and the different populations appear to have undergone genetic adaptation of their thermal sensitivity to the varied thermal environments.

Animals↗

[Challenges facing Caribbean countries 10 years after the International Conference on Population and Development in Cairo, Egypt].

At the International Conference on Population and Development (ICPD) that was held in Cairo, Egypt, in 1994, participants acknowledged that population, economic growth, and sustainable development are concepts that are closely linked, and important strides were made in terms of increased recognition of sexual and reproductive rights. The Programme of Action ratified at that Conference was adopted as a platform for designing national and international policies in the areas of population and development for a period of twenty years. However, in Latin America and the Caribbean all types of obstacles-financial, institutional, and human-still stand in the way of attaining the goals of the Programme of Action, and some governments have established measures that undermine their people's exercise of sexual and reproductive rights. The Caribbean Subregional Meeting to Assess the Implementation of the Programme of Action of the International Conference on Population and Development 10 Years after its Adoption was held in Port of Spain, Trinidad and Tobago, in November of 2003. At the meeting, which was attended by representatives from 20 Caribbean countries and territories, a call was made for more rational use of available resources and for mobilization of additional funds for developing and implementing population and development programs and policies in the Caribbean. The meeting also saw the approval of the Caribbean Declaration, which lays out the challenges that should serve as the roadmap for taking actions to consolidate the progress achieved so far and come closer to attaining the goals established by the ICPD. In the Declaration, the countries and territories of the Caribbean asserted their commitment to continue legislative reforms at the national level while seeking to enforce these reforms in an effort to ensure implementation of the ICPD's Programme of Action and of the Caribbean Plan of Action for Population and Development that was adopted in 1996 by the Economic Community for Latin America and the Caribbean.

Caribbean Region↗

RNase P: a promising molecular target for the development of new drugs.

RNase P is an ubiquitous and essential endonuclease in tRNA biogenesis, which generates the mature 5'-termini of tRNAs. RNase P activities have been identified in all three kingdoms of life (Bacteria, Archaea, Eukarya). Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA and protein subunits. In bacteria and in some archaea, the catalytic function of this enzyme resides entirely in its RNA subunit, which is one of firstly identified ribozymes. Its high structural and functional diversity among representatives of a vast variety of phylogenetic domains indicates that RNase P could also serve as a molecular target of and a useful screening system for the biological activity of different compounds and give more insight into the molecular mechanisms of their action inside the cell. The emerged information from recent studies on the mechanism and structural idiosyncrasies of RNase P provides a convenient platform for designing specific inhibitors for this ribozyme and potential areas of its application in gene therapy. This review summarises the current information on the effect of several protein synthesis inhibitors, retinoids and arotinoids, vitamin D analogues and anthalin on the activity of RNase P.

Aminoglycosides↗

Microarray and nanotechnology applications of functional nanoparticles.

Microarrays are a sensitive, specific, miniaturized devices that may be used to detect selected DNA sequences and proteins, or mutated genes associated with human diseases. Several methods have been developed to detect the binding of complementary molecules to microarrays by generating an optical signal. One of the most commonly used molecular labeling methods at present is fluorescence, but its application is expensive due to sophisticated equipment required to design the platform, hybridize it, and interpret the images derived from microarray-based studies. This is a drawback for its use in laboratories and clinical services. Another less expensive procedure having similar sensitivity and specificity is DNA and protein functional nanoparticles (FNP). Nanoparticles are sphere-like biocompatible materials made of inert silica, metal or crystals of a nanometer in size, which are generally coated with a thin gold layer. They may be used as hybridization probes in single nucleotide polymorphism (SNP) screening and to detect biological markers for cancer, infection, and cardiovascular diseases.

Biomarkers↗