Towards an Analytical Biology.

This article draws a perspective on the increasingly unavoidable question of whether steps can be taken in genomics and biology at large to move them more rapidly towards more analytical and deductive biology, akin to similar developments that occurred in other natural sciences, such as physics and chemistry, centuries ago. It provides a summary of recent advances in other relevant sciences in the last 3 decades that are likely to pull it in that direction in the next decade or so, as well as what methods and tools will make it possible.

Calcium sensing and signaling are impaired in the lumbar spine of a rat model of congenital kyphosis.

PURPOSE: Kyphosis involves spines curving excessively backward beyond their physiological curvature. Although the normal structure of the spinal vertebrae is extremely important for maintaining posture and the normal function of the thoracic and abdominal organs, our knowledge concerning the pathogenesis of the disease is insufficient. We herein report that the downregulation of the calcium signaling pathway is involved in the pathogenesis of congenital kyphosis. METHODS: The third to fifth lumbar spine segments, the kyphotic region of Ishibashi (IS) rats, which are used as a model of congenital kyphoscoliosis, were collected. A DNA microarray, quantitative PCR, Western blotting, and immunohistochemistry were used to measure the expression of genes and proteins related to intracellular calcium signaling. RESULTS: We found that the expression of calcium-sensing receptor (CaSR) and transient receptor potential vanilloid 1 (Trpv1)-two receptors involved in the calcium signaling-was decreased in the lumbar spine of IS rats. We also observed that the number of CaSR-immunoreactive and Trpv1-immunoreactive cells in the lumbar spine of IS rats was lower than in wild-type rats. Furthermore, the expression of intracellular molecules downstream of these receptors, such as phosphorylated protein kinase C, c-Jun N-terminal kinase, and neural EGFL-like 1, was also reduced. In fact, the calcium content in the lumbar spine of IS rats was significantly lower than that in wild-type rats. CONCLUSION: These results indicate that adequate calcium signaling is extremely important for the regulation of normal bone formation and may also be a key factor for understanding the pathogenesis of congenital kyphosis.

Characterisation of Methicillin-Resistant Staphylococcus aureus from Alexandria, Egypt.

The present study aims to characterise clinical MRSA isolates from a tertiary care centre in Egypt's second-largest city, Alexandria. Thirty isolates collected in 2020 were genotypically characterised by microarray to detect their resistance and virulence genes and assign them to clonal complexes (CC) and strains. Isolates belonged to 11 different CCs and 14 different strains. CC15-MRSA-[V+fus] (n = 6), CC1-MRSA-[V+fus+tir+ccrA/B-1] (PVL+) (n = 5) as well as CC1-MRSA-[V+fus+tir+ccrA/B-1] and CC1153-MRSA-[V+fus] (PVL+) (both with n = 3) were the most common strains. Most isolates (83%) harboured variant or composite SCCmec V or VI elements that included the fusidic acid resistance gene fusC. The SCCmec [V+fus+tir+ccrA/B-1] element of one of the CC1 isolates was sequenced, revealing a presence not only of fusC but also of blaZ, aacA-aphD and other resistance genes. PVL genes were also common (40%). The hospital-acquired MRSA CC239-III strain was only found twice. A comparison to data from a study on strains collected in 2015 (Montelongo et al., 2022) showed an increase in fusC and PVL carriage and a decreasing prevalence of the CC239 strain. These observations indicate a diffusion of community-acquired strains into hospital settings. The beta-lactam use in hospitals and the widespread fusidic acid consumption in the community might pose a selective pressure that favours MRSA strains with composite SCCmec elements comprising mecA and fusC. This is an unsettling trend, but more MRSA typing data from Egypt are required.

An Algorithm-optimized Scheme for In situ Synthesis of DNA Microarrays.

BACKGROUND: The cost of synthetic DNA has limited applications in frontier science and technology fields such as synthetic biology, DNA storage, and DNA chips. OBJECTIVE: The objective of this study is to find an algorithm-optimized scheme for the in situ synthesis of DNA microarrays, which can reduce the cost of DNA synthesis. METHODS: Here, based on the characteristics of in situ chemical synthesis of DNA microarrays, an optimization algorithm was proposed. Through data grading, the sequences with the same base at as many different features as possible were synthesized in parallel to reduce synthetic cycles. RESULTS AND DISCUSSION: The simulation results of 10 and 100 randomly selected sequences showed that when level=2, the reduction ratio in the number of synthetic cycles was the largest, 40% and 32.5%, respectively. Subsequently, the algorithm-optimized scheme was applied to the electrochemical synthesis of 12,000 sequences required for DNA storage. The results showed that compared to the 508 cycles required by the conventional synthesis scheme, the algorithmoptimized scheme only required 342 cycles, which reduced by 32.7%. In addition, the reduced 166 cycles reduced the total synthesis time by approximately 11 hours. CONCLUSIONS: The algorithm-optimized synthesis scheme can not only reduce the synthesis time of DNA microarrays and improve synthesis efficiency, but more importantly, it can also reduce the cost of DNA synthesis by nearly 1/3. In addition, it is compatible with various in situ synthesis methods of DNA microarrays, including soft-lithography, photolithography, a photoresist layer, electrochemistry and photoelectrochemistry. Therefore, it has very important application value.

High-Resolution Chrono-Transcriptome of Lactococcus lactis Reveals That It Expresses Proteins with Adapted Size and pI upon Acidification and Nutrient Starvation.

Whole-genome transcriptional analyses performed on microorganisms are traditionally based on a small number of samples. To map transient expression variations, and thoroughly characterize gene expression throughout the growth curve of the widely used model organism Lactococcus lactis MG1363, gene expression data were collected with unprecedented time resolution. The resulting gene expression patterns were globally analyzed in several different ways to demonstrate the richness of the data and the ease with which novel phenomena can be discovered. When the culture moves from one growth phase to another, gene expression patterns change to such an extent that we suggest that those patterns can be used to unequivocally distinguish growth phases from each other. Also, within the classically defined growth phases, subgrowth phases were distinguishable with a distinct expression signature. Apart from the global expression pattern shifts seen throughout the growth curve, several cases of short-lived transient gene expression patterns were clearly observed. These could help explain the gene expression variations frequently observed in biological replicates. A method was devised to estimate a measure of unnormalized/absolute gene expression levels and used to determine how global transcription patterns are influenced by nutrient starvation or acidification of the medium. Notably, we inferred that L. lactis MG1363 produces proteins with on average lower pIs and lower molecular weights as the medium acidifies and nutrients get scarcer. IMPORTANCE This data set is a rich resource for microbiologists interested in common mechanisms of gene expression, regulation and in particular the physiology of L. lactis. Thus, similar to the common use of genome sequence data by the scientific community, the data set constitutes an extensive data repository for mining and an opportunity for bioinformaticians to develop novel tools for in-depth analysis.

Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes.

Exposure to Endocrine Disrupting Chemicals (EDC) has been linked with several adverse outcomes. In this review, we examine EDCs that are pervasive in the environment and are of concern in the context of human, animal, and environmental health. We explore the consequences of EDC exposure on aquatic life, terrestrial animals, and humans. We focus on the exploitation of genomics technologies and in particular whole transcriptome sequencing. Genome-wide analyses using RNAseq provides snap shots of cellular, tissue and whole organism transcriptomes under normal physiological and EDC perturbed conditions. A global view of gene expression provides highly valuable information as it uncovers gene families or more specifically, pathways that are affected by EDC exposures, but also reveals those that are unaffected. Hypotheses about genes with unknown functions can also be formed by comparison of their expression levels with genes of known function. Risk assessment strategies leveraging genomic technologies and the development of toxicology databases are explored. Finally, we review how the Adverse Outcome Pathway (AOP) has exploited this high throughput data to provide a framework for toxicology studies.

Spinal malformation - A biochemical analysis using congenital kyphosis rats.

Spinal kyphosis involves the vertebrae curving excessively backward, beyond their physiological curvature. Although the normal structure of the spinal vertebrae is extremely important for maintaining posture, the normal function of the thoracic and abdominal organs, and cosmetics, our knowledge concerning the pathogenesis of this disease is lacking. Furthermore, the responsible gene has not yet been identified. In this short review, we summarize the current state of kyphosis research and introduce the molecular and cellular mechanisms associated with the pathogenesis of this disease, based on findings obtained using rats that develop kyphosis.

Multicenter retrospective study on the use of Curebest™ 95GC Breast for estrogen receptor-positive and node-negative early breast cancer.

BACKGROUND: The benefits of postoperative chemotherapy in patients with estrogen receptor (ER)-positive breast cancer remain unclear. The use of tumor grade, Ki-67, or ER expression failed to provide an accurate prognosis of the risk of relapse after surgery in patients. This study aimed to evaluate whether a multigene assay Curebest™ 95GC Breast (95GC) can identify the risk of recurrence and provide more insights into the requirements for chemotherapy in patients. METHODS: This single-arm retrospective multicenter joint study included patients with ER-positive, node-negative breast cancer who were treated at five facilities in Japan and had received endocrine therapy alone as adjuvant therapy. The primary lesion specimens obtained during surgery were analyzed using the 95GC breast cancer multigene assay. Based on the 95GC results, patients were classified into low-risk (95GC-L) and high-risk (95GC-H) groups. RESULTS: The 10-year relapse-free survival rates were 88.4 and 59.6% for the 95GC-L and 95GC-H groups, respectively. Histologic grade, Ki-67, and PAM50 exhibited a significant relationship with the 95GC results. The segregation into 95GC-L and 95GC-H groups within established clinical factors can identify subgroups of patients using histologic grade or PAM50 classification with good prognosis without receiving chemotherapy. CONCLUSIONS: Based on the results of our retrospective study, 95GC could be used to evaluate the long-term prognosis of ER-positive, node-negative breast cancer. Even though further prospective validation is necessary, the inclusion of 95GC in clinical practice could help to select optimal treatments for breast cancer patients and identify those who do not benefit from the addition of chemotherapy, thus avoiding unnecessary treatment.

Meta-Analysis-Assisted Detection of Gravity-Sensitive Genes in Human Vascular Endothelial Cells.

Gravity affects the function and maintenance of organs, such as bones, muscles, and the heart. Several studies have used DNA microarrays to identify genes with altered expressions in response to gravity. However, it is technically challenging to combine the results from various microarray datasets because of their different data structures. We hypothesized that it is possible to identify common changes in gene expression from the DNA microarray datasets obtained under various conditions and methods. In this study, we grouped homologous genes to perform a meta-analysis of multiple vascular endothelial cell and skeletal muscle datasets. According to the t-distributed stochastic neighbor embedding (t-SNE) analysis, the changes in the gene expression pattern in vascular endothelial cells formed specific clusters. We also identified candidate genes in endothelial cells that responded to gravity. Further, we exposed human umbilical vein endothelial cells (HUVEC) to simulated microgravity (SMG) using a clinostat and measured the expression levels of the candidate genes. Gene expression analysis using qRT-PCR revealed that the expression level of the prostaglandin (PG) transporter gene SLCO2A1 decreased in response to microgravity, consistent with the meta-analysis of microarray datasets. Furthermore, the direction of gravity affected the expression level of SLCO2A1, buttressing the finding that its expression was affected by gravity. These results suggest that a meta-analysis of DNA microarray datasets may help identify new target genes previously overlooked in individual microarray analyses.

Structure and Oligonucleotide Binding Efficiency of Differently Prepared Click Chemistry-Type DNA Microarray Slides Based on 3-Azidopropyltrimethoxysilane.

The structural characterization of glass slides surface-modified with 3-azidopropyltrimethoxysilane and used for anchoring nucleic acids, resulting in the so-called DNA microarrays, is presented. Depending on the silanization conditions, the slides were found to show different oligonucleotide binding efficiency, thus, an attempt was made to correlate this efficiency with the structural characteristics of the silane layers. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and X-ray reflectometry (XRR) measurements provided information on the surface topography, chemical composition and thickness of the silane films, respectively. The surface for which the best oligonucleotides binding efficiency is observed, has been found to consist of a densely-packed silane layer, decorated with a high-number of additional clusters that are believed to host exposed azide groups.

Single-Step Printable Hydrogel Microarray Integrating Long-Chain DNA for the Discriminative and Size-Specific Sensing of Nucleic Acids.

A simple approach to fabricating hydrogel-based DNA microarrays is reported by physically entrapping the rolling circle amplification (RCA) product inside printable in situ gelling hydrazone cross-linked poly(oligoethylene glycol methacrylate) hydrogels. The hydrogel-printed RCA microarray facilitates improved RCA immobilization (>65% even after vigorous washing) and resistance to denaturation relative to RCA-only printed microarrays in addition to size-discriminative sensing of DNA probes (herein, 27 or fewer nucleotides) depending on the internal porosity of the hydrogel. Furthermore, the high number of sequence repeats in the concatemeric RCA product enables high-sensitivity detection of complementary DNA probes without the need for signal amplification, with signal/noise ratios of 10 or more achieved over a short 30 min assay time followed by minimal washing. The inherent antifouling properties of the hydrogel enable discriminative hybridization in complex biological samples, particularly for short (∼10 nt) oligonucleotides whose hybridization in other assays tends to be transient and of low affinity. The scalable manufacturability and efficient performance of these hydrogel-printed RCA microarrays thus offer potential for rapid, parallel, and inexpensive sensing of short DNA/RNA biomarkers and ligands, a critical current challenge in diagnostic and affinity screening assays.

Cytogenetics in the genomic era.

Haematological neoplasms are characterised by the presence of recurrent chromosomal abnormalities, making cytogenetics essential for establishing the diagnosis and prognosis. Chromosome banding analysis is mandatory for chronic myeloid leukaemia, neoplasms with eosinophilia, myelodysplastic syndromes and acute leukaemias. In contrast, in other myeloid neoplasms, chronic lymphocytic leukaemia, non-Hodgkin lymphoma and multiple myeloma, the study must be complemented with fluorescence in situ hybridization and/or microarrays, which can overcome some of the shortcomings of banding analysis to identify potential cryptic alterations or reciprocal translocations. In the genomic era, novel technologies such as next generation sequencing are now being used in clinical routine analysis, since they offer the possibility of studying mutations and copy number alterations in a single study at a higher resolution and/or sensitivity. However, they require highly qualified staff and further standardisation, especially regarding data analysis, thereby limiting their current applicability.

Gene expression analysis identifies hypothetical genes that may be critical during the infection process of Xanthomonas citri subsp. citri

Background: Gene expression analysis via microarray is widely used in phytobacteria to validate differential gene expression associated with virulence or to compare biological profiles of wild type and mutant strains. Here, we employed DNA microarrays to study the early stages of the infection process (24, 72 and 120 h post-inoculation) of Xanthomonas citri subsp. citri (Xac) infecting Citrus sinensis to interrogate the expression profiles of hypothetical genes. Results: Under infective conditions, 446 genes were up- and 306 downregulated. Outstanding among genes upregulated during infection were those involved in synthesizing the Type 3 Secretion System and effectors, xanthan gum and quorum-sensing induction, and flagellum synthesis and regulation. Additionally, 161 hypothetical genes were up- and 100 were downregulated, 49 of which are known to have a significant biological role. To understand hypothetical gene co-regulation or -expression, nine expression profiles including 158 genes were identified during the three infection phases. Of these, 47 hypothetical genes were identified as having expression profiles associated with at least one connected to a gene associated with adaptation and virulence. Conclusions: Expression patterns of six differentially expressed genes were validated by quantitative reverse transcription polymerase chain reaction, thus demonstrating the effectiveness of this tool in global gene expression analysis in Xac.

Applying microarray-based technique to study and analyze silkworm (Bombyx mori) transcriptomic response to long-term high iron diet.

To investigate the biological processes affected by long-term iron supplementation, newly hatched silkworms were exposed to high iron mulberry diet (10 and 100 ppm) and its effect on silkworm transcriptom was determined. The results showed that the silkworm was responsive to iron by increasing iron concentration and ferritin levels in the hemolymph and by regulating the expression of many other genes. A total of 523 and 326 differentially expressed genes were identified in 10 and 100 ppm Fe group compared to the control, respectively. Of these genes, 249 were shared between in both the 10 ppm and 100 ppm Fe group, including 152 up-regulated and 97 down-regulated genes. These shared genes included 19 known Fe regulated, 24 immune-related, 12 serine proteases and serine proteases homologs, 41 cuticular and cuticle genes. Ten genes (carboxypeptidases A, serine protease homologs 85, fibrohexamerin/P25, transferrin, sex-specific storage-protein 2, fungal protease inhibitor F, insect intestinal mucin, peptidoglycan recognition protein B, cuticle protein CPH45, unknown gene) were involved in the regulation of iron overload responses.

Complejidad de la expresión de genes asociados a obesidad en el tejido adiposo humano / Complexity of the expression of genes associated with obesity in human adipose tissue / Complexidade da expressão de genes associados à obesidade no tecido adiposo humano

Resumen Objetivo: Analizar la complejidad de la expresión génica en tejido adiposo de genes asociados con obesidad, mediante simulación computacional con diferentes herramientas bioinformáticas. Métodos: Después de una búsqueda bibliográfica en PubMed, se seleccionaron 37 genes asociados con obesidad con fold change mayor a 1,5. A partir del cálculo de valores de los z-score obtenidos de experimentos de micromatrices de ADN de muestras de tejido adiposo de personas obesas y de control, se construyó una red de interacción con el programa Cytoscape 3.2. La información detallada sobre las características genómicas de estos genes se extrajo de las bases de datos Genome Browser de la UCSC y del NCBI. Utilizando herramientas de análisis de multivariado, se hizo un análisis de componentes principales y uno de agrupación. Resultados: La red construida mostró que los genes con mayor número de interacciones fueron: 1) el factor nuclear respiratorio (NRF1), 2) el canal activado de potasio activado por calcio alfa 1 (KCNMA1) y 3) la sintasa de ácidos grasos (FASN). Los que tuvieron mayores valores de expresión fueron: 1) el factor de crecimiento endotelial vascular A (VEGFA), 2) la dioxigenasa dependiente de alfa-cetoglutarato (FTO) y 3) el regulador de crecimiento neuronal 1 (NEGR1). Las proteínas IL6, BDNF y HLC tuvieron los mayores valores de interacción con IL6R, NRF1 y ACACB, respetivamente. Las categorías ontológicas más importantes se relacionaron con procesos metabólicos de lipoproteínas, el ciclo de los ácidos tricarboxílicos, la activación de las MAP-quinasas y la cascada JNK. Conclusiones: En su conjunto los resultados obtenidos de sobreexpresión diferencial de genes asociados con el metabolismo de lípidos en el tejido adiposo de personas obesas podría ser un criterio para discriminar a nivel de diagnóstico esta patología.

Summary Objective: To analyze the complexity of gene expression in the adipose tissue of genes associated with obesity, by computer simulation with different bioinformatics tools. Methods: After conducting a PubMed literature search, 37 genes associated with obesity with a fold change greater than 1.5 were selected. An interaction network was cons tructed using the Cytoscape 3.2 program from the calculation of z-score values obtained from DNA microarray experiments of adipose tissue samples collected from obese and control people. Detailed information on the genomic characteristics of these genes was extracted from the UCSC and NCBI Genome Browser databases. Using multivariate analysis tools, a principal component analysis and a cluster analysis were carried out. Results: The constructed network showed that the genes with the greatest number of interactions were: 1) the nuclear respiratory factor (NRF1), 2) the activated channel of potassium activate by calcium alpha 1 (KCNMA1), and 3) the fatty acid synthase (FASN). Those with the higher expression values were: 1) vascular endothelial growth factor A (VEGFA), 2) alpha-ketoglutarate-dependent dioxygenase (FTO), and 3) neuronal growth regulator 1 (NEGR1). The IL6, BDNF and HLC proteins had the highest interaction values with IL6R, NRF1 and ACACB, respectively. The most important ontological categories were related to lipoprotein metabolic processes, the tricarboxylic acid cycle, the activation of the MAP kinases, and the JNK cascade. Conclusions: As a whole, the results obtained from differential overexpression of genes associated with lipid metabolism in the adipose tissue of obese people could be a criterion to discriminate this pathology at a diagnostic level.

Resumo Objetivo: Analisar a complexidade da expressão gênica no tecido adiposo de genes associados com obesidade, por meio de simulação por computador com diferentes ferramentas bioinformáticas. Métodos: Após uma busca bibliográfica em PubMed, foram selecionados 37 genes associados com obesidade com fold change superior a 1,5. A partir do cálculo de valores dos z-score obtidos de experimentos de micro matrizes de ADN de amostras de tecido adiposo de pessoas obesas e de controle, construiu-se uma rede de interação com o programa Cytoscape 3.2. A informação detalhada sobre as características genômicas destes genes foi obtida das bases de dados Genome Browser da UCSC e do NCBI. Utilizando ferramentas de análise de multivariado, fez-se uma análise de componentes principais e um de agrupação. Resultados: A rede construída mostrou que os genes com maior número de interações foram: 1) o fator nuclear respiratório (NRF1), 2) o canal ativado de potássio ativado por cálcio alfa 1 (KCNMA1) e 3) ácido graxo sintase (FASN). Os que tiveram maiores valores de expressão foram: 1) o fator de crescimento endo-telial vascular A (VEGFA), 2) a dioxigenase dependente de alfa-cetoglutarato (FTO) e 3) o regulador de crescimento neuronal 1 (NEGR1). As proteínas IL6, BDNF e HLC tiveram os maiores valores de interação com IL6R, NRF1 e ACACB, respectivamente. As categorias ontológicas mais importantes se relacionaram com processos metabólicos de lipoproteínas, o ciclo dos ácidos tri carboxílicos, a ativação das MAP-quinases e a cascata JNK. Conclusões: Em seu conjunto, os resultados obtidos de superexpressão diferencial de genes associados com o metabolismo de lipídios no tecido adiposo de pessoas obesas poderia ser um critério para discriminar a nível de diagnóstico esta patologia.

Resveratrol induces dynamic changes to the microglia transcriptome, inhibiting inflammatory pathways and protecting against microglia-mediated photoreceptor apoptosis.

Microglia activation is central to the pathophysiology of retinal degenerative disorders. Resveratrol, a naturally occurring non-flavonoid phenolic compound present in red wine has potent anti-inflammatory and immunomodulatory properties. However, molecular mechanisms by which resveratrol influences microglial inflammatory pathways and housekeeping functions remain unclear. Here, we first studied the immuno-modulatory effects of resveratrol on BV-2 microglial cells at the transcriptome level using DNA-microarrays and selected qRT-PCR analyses. We then analyzed resveratrol effects on microglia morphology, phagocytosis and migration and estimated their neurotoxicity on 661 W photoreceptors by quantification of caspase 3/7 levels. We found that resveratrol effectively blocked gene expression of a broad spectrum of lipopolysaccharide (LPS)-induced pro-inflammatory molecules, including cytokines and complement proteins. These transcriptomic changes were accompanied by potent inhibition of LPS-induced nitric oxide secretion and reduced microglia-mediated apoptosis of 661 W photoreceptor cultures. Our findings highlight novel targets involved in the anti-inflammatory and neuroprotective action of resveratrol against neuroinflammatory responses.

Expression profiling of cell-intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages.

BACKGROUND: Differentiation of human induced pluripotent stem cells (hiPSCs) into retinal lineages offers great potential for medical application. Therefore, it is of crucial importance to know the key intrinsic regulators of differentiation and the specific biomarker signatures of cell lineages. METHODS: In this study, we used microarrays to analyze transcriptomes of terminally differentiated retinal ganglion cell (RGC) and retinal pigment epithelium (RPE) lineages, as well as intermediate retinal progenitor cells of optic vesicles (OVs) derived from hiPSCs. In our analysis, we specifically focused on the classes of transcripts that encode intrinsic regulators of gene expression: the transcription factors (TFs) and epigenetic chromatin state regulators. We applied two criteria for the selection of potentially important regulators and markers: firstly, the magnitude of fold-change of upregulation; secondly, the contrasted pattern of differential expression between OV, RGC and RPE lineages. RESULTS: We found that among the most highly overexpressed TF-encoding genes in the OV/RGC lineage were three members of the Collier/Olfactory-1/Early B-cell family: EBF1, EBF2 and EBF3. Knockdown of EBF1 led to significant impairment of differentiation of hiPSCs into RGCs. EBF1 was shown to act upstream of ISL1 and BRN3A, the well-characterized regulators of RGC lineage specification. TF-encoding genes DLX1, DLX2 and INSM1 were the most highly overexpressed genes in the OVs, indicating their important role in the early stages of retinal differentiation. Along with MITF, the two paralogs, BHLHE41 and BHLHE40, were the most robust TF markers of RPE cells. The markedly contrasted expression of ACTL6B, encoding the component of chromatin remodeling complex SWI/SNF, discriminated hiPSC-derived OV/RGC and RPE lineages. CONCLUSIONS: We identified novel, potentially important intrinsic regulators of RGC and RPE cell lineage specification in the process of differentiation from hiPSCs. We demonstrated the crucial role played by EBF1 in differentiation of RGCs. We identified intrinsic regulator biomarker signatures of these two retinal cell types that can be applied with high confidence to confirm the cell lineage identities.

The contribution of DNA microarray technology to gene expression profiling in Leishmania spp.: A retrospective view.

The first completed genome project of any living organism, excluding viruses, was of the gammaproteobacteria Haemophilus influenzae in 1995. Until the last decade, genome sequencing was very tedious because genome survey sequences (GSS) and/or expressed sequence tags (ESTs) belonging to plasmid, cosmid, and artificial chromosome genome libraries had to be sequenced and assembled in silico. No genome is completely assembled because gaps and unassembled contigs are always remaining. However, most represent an organism's whole genome from a practical point of view. The first genome sequencing projects of trypanosomatid parasites Leishmania major, Trypanosoma cruzi, and T. brucei were completed in 2005 following those strategies. The functional genomics era developed on the basis of microarray technology and has been continuously evolving. In the case of the genus Leishmania, substantial information about differentiation in the digenetic life cycle of the parasite has been obtained. More recently, next generation sequencing has revolutionized genome sequencing and functional genomics, leading to more sensitive and accurate results by using much fewer resources. Though this new technology is more advantageous, it does not invalidate microarray results. In fact, promising vaccine candidates and drug targets have been found by means of microarray-based screening and preliminary proof-of-concept tests.

Gene Meter: Accurate abundance calculations of gene expression.

We previously reported that thousands of transcripts in the mouse and zebrafish significantly increased in abundance in a time series spanning from life to several days after death. Transcript abundances were determined by: calibrating each microarray probe using a dilution series of pooled RNAs, fitting the probe-responses to adsorption models, and back-calculating abundances using the probe signal intensity of a sample and the best fitting model. The accuracy of the abundance measurements was not assessed in our previous study because individual transcript concentrations in the calibration pool were not known. Accurate transcript abundances are highly desired for modeling the dynamics of biological systems and investigating how systems respond to perturbations. In this study, we show that accurate transcript abundances can be determined by calibrating the probes using a calibration pool of transcripts with known concentrations. Instructions for determining accurate transcript abundances using the Gene Meter approach are provided.

Gene-Set Reduction for Analysis of Major and Minor Gleason Scores Based on Differential Gene-Set Expressions and Biological Pathways in Prostate Cancer.

The Gleason score (GS) plays an important role in prostate cancer detection and treatment. It is calculated based on a sum between its major and minor components, each ranging from 1 to 5, assigned after examination of sample cells taken from each side of the prostate gland during biopsy. A total GS of at least 7 is associated with more aggressive prostate cancer. However, it is still unclear how prostate cancer outcomes differ for various distributions of GS between its major and minor components. This article applies Significance Analysis of Microarray for Gene-Set Reduction to a real microarray study of patients with prostate cancer and identifies 13 core genes differentially expressed between patients with a major GS of 3 and a minor GS of 4, or (3,4), vs patients with a combination of (4,3), starting from a less aggressive GS combination of (3,3), and moving toward a more aggressive one of (4,4) via gray areas of (3,4) and (4,3). The resulting core genes may improve understanding of prostate cancer in patients with a total GS of 7, the most common grade and most challenging with respect to prognosis.