Search

Detection of brain-specific miRNAs in the peripheral blood could serve as a surrogate marker of traumatic brain injury (TBI). Here, we systematically identified brain-enriched miRNAs, and tested their utility as TBI biomarkers in the acute phase of care. Publically available microarray data generated from 29 postmortem human tissues were used to rank 1,364 miRNAs in terms of their degree of brain-specific expression. Levels of the top six ranked miRNAs were then prospectively measured in serum samples collected from 10 Patients with TBI at hospital admission, as well as from 10 controls. The top six miRNAs identified in our analysis (miR-124-3p, miR-219a-5p, miR-9-5p, miR-9-3p, miR-137, and miR-128-3p) were enriched 70 to 320-fold in brain relative to other tissues, and exhibited dramatically greater brain specificity compared to several miRNAs previously proposed as biomarkers. Furthermore, their levels were elevated in serum from patients with TBI compared to controls, and could collectively discriminate between groups with 90% sensitivity and 100% specificity. Interestingly, subsequent informatic pathway analysis revealed that their target transcripts were enriched for components of signaling pathways active in peripheral organs involved in common post-TBI complications. The six candidate miRNAs identified in this preliminary study have promise as blood biomarkers of TBI, and could also be molecular contributors to systemic physiologic changes commonly observed post-injury. [ABSTRACT FROM AUTHOR]

Various bioactive polyketides have been found in Aloe barbadensis. However, the polyketide synthases (PKSs), which participate in biosynthesis of polyketides in A. barbadensis remain unknown. In this study, two type III PKSs (AbPKS1 and AbPKS2) were identified from A. barbadensis. AbPKS1 and AbPKS2 were able to utilize malonyl-CoA to yield heptaketides (TW93a and aloesone) and octaketides (SEK4 and SEK4b), respectively. AbPKS1 also exhibited catalytic promiscuity in recognizing CoA thioesters of aromatics to produce unusual polyketides. What Is more, a whole cell biocatalysis system with the capability of producing 26.4 mg/L of SEK4/SEK4b and 2.1 mg/L of aloesone was successfully established. [ABSTRACT FROM AUTHOR]

Objective: Dual diagnosis (DD) is the co-occurrence of at least one substance use disorder and one or more mental disorders in a given individual. Despite this comorbidity being highly prevalent and associated with adverse clinical outcomes, its neurobiology remains unclear. Furthermore, patients with DD are at higher risk for suicidal behavior in comparison with single disorder patients. Our objective was to evaluate brain gene expression patterns in individuals with DD who died by suicide. Methods: We compared the gene expression profile in the dorsolateral prefrontal cortex of suicides with DD (n = 10) to the transcriptome of suicides with substance use disorder alone (n = 10), suicides with mood disorders (MD) alone (n = 13), and suicides without mental comorbidities (n = 5). Gene expression profiles were assessed by microarrays. In addition, we performed a brain cell type enrichment to evaluate whether the gene expression profiles could reflect differences in cell type compositions among the groups. Results: When comparing the transcriptome of suicides with DD to suicides with substance use disorder alone and suicides with MD alone, we identified 255 and 172 differentially expressed genes (DEG), respectively. The overlap of DEG between both comparisons (112 genes) highlighted the presence of common disrupted pathways in substance use disorder and MD. When comparing suicides with DD to suicides without mental comorbidities, we identified 330 DEG, mainly enriched in neurogenesis. Cell type enrichment indicated higher levels of glial markers in suicides with DD compared to the other groups. Conclusions: Suicides with DD exhibited a gene expression profile distinct from that of suicides with a single disorder, being substance use disorder or MD, and suicides without mental disorders. Our results suggest alteration in the expression of genes involved in glial specific markers, glutamatergic and GABAergic neurotransmission in suicides with DD compared to suicides with a single disorder and suicides without mental comorbidities. Alterations in the expression of synaptic genes at different levels were found in substance use disorder and MD. [ABSTRACT FROM AUTHOR]

UDP-glucose 4-epimerase (UGE) is a universal enzyme responsible for interconversion of UDP-glucose and UDP-galactose. However, the gene encoding UGE from Davallia divaricate is elusive. In this study, two UGE genes, ddUGE1 and ddUGE2, were isolated and cloned from D. divaricate using a transcriptome-guided search strategy. Two unigenes sharing high sequence identity with UGE homologous genes were selected from transcriptome assembly. The enzymes, further functionally expressed in Escherichia coli, exhibit narrow substrate specificity. The biochemical characterization assays of DdUGE1 and DdUGE2 showed good thermal and pH stability, and metal ion independence, which provides a meaningful feature for biotechnological applications. [ABSTRACT FROM AUTHOR]

Objective: As a frequent hypertensive disorder in pregnancy, preeclampsia causes 15% of all preterm deliveries. This study aims to understand its mechanism via analyzing gene expression and methylation data.Methods: Human gene expression microarray data (GSE73374) and corresponding DNA methylation microarray data (GSE73375) of preeclamptic placental tissues (n = 19) and normotensive placental tissues (n = 17) were obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs), differentially methylated regions (DMRs) and CpG islands (DMIs) were identified and compared. Pathway enrichment analysis was performed, and the functional interactions were investigated.Results: A total of 392 DEGs, 2667 DMRs, and 464 DMIs were found between the two groups, and a functional interaction network of DEGs was established. Then, 28 potential key genes were identified, which were oppositely regulated in preeclampsia regarding expression and methylation. Eight of the potential key genes had DMIs, among which ITGA5 interacted with FN1 and FOS. The 3 DEGs were up-regulated, and their DMIs were hypomethylated.Conclusion: FN1, FOS, and ITGA5 might promote the development of preeclampsia via modulating differentiation/apoptosis/invasion of human extravillous trophoblasts, as well as focal adhesion, VEGFR3 signaling, β1 integrin cell surface interactions, α9β1/α4β1 integrin signaling, AP-1/ATF-2/HIF-1α transcription factor networks, and Fc-epsilon receptor I signaling in mast cells. [ABSTRACT FROM AUTHOR]

Introduction: Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests. [ABSTRACT FROM AUTHOR]

Purpose/Aim: We sought to identify the anteroposterior spatial gene expression hierarchy in the human sclera to develop a hypothesis for axial elongation and deformity of the eyeball. Materials and Methods: We analyzed the global gene expression of human scleral cells derived from distinct parts of the human infant sclera obtained from surgically enucleated eyes with retinoblastoma, using Affymetrix GeneChip oligonucleotide arrays, and compared, in particular, gene expression levels between the anterior and posterior parts of the sclera. The ages of three donors were 10M, 4M, and 1Y9M. Results: K-means clustering analysis of gene expression revealed that expression levels of cartilage-associated genes such asCOLXIAandACANincreased from the anterior to the posterior part of the sclera. Microarray analyses and RT-PCR data showed that the expression levels ofMGP, COLXIA, BMP4, andRARBwere significantly higher in the posterior than in the anterior sclera of two independent infant eyes. Conversely, expression levels ofWNT2, DKK2, GREM1, andHOXB2were significantly higher in the anterior sclera. Among several Wnt-family genes examined,WNT2Bwas found to be expressed at a significantly higher level in the posterior sclera, and the reverse order was observed forWNT2. The results of luciferase reporter assays suggested that a GSK-3β inhibitor stimulated Wnt/β-catenin signaling particularly strongly in the posterior sclera. The expression pattern ofRARB, a myopia-related gene, was similar in three independent eyes. Conclusions: Chondrogenic potential was higher and Wnt/β-catenin signaling was more potently activated by a GSK-3β inhibitor in the posterior than in the anterior part of the human infant sclera. Although the differences in the gene expression profiles between the anterior and posterior sclera might be involved only in normal growth processes, this anteroposterior hierarchy in the sclera might contribute to disorders involving abnormal elongation and deformity of the eyeball, including myopia. [ABSTRACT FROM PUBLISHER]

6-MSITC and 6-MTITC are sulforaphane (SFN) analogs found in Japanese Wasabi. As we reported previously, Wasabi isothiocyanates (ITCs) are activators of Nrf2-antioxidant response element pathway, and also inhibitors of pro-inflammatory cyclooxygenase-2. This study is the first to assess the global changes in transcript levels by Wasabi ITCs, comparing with SFN, in HepG2 cells. We performed comparative gene expression profiling by treating HepG2 cells with ITCs, followed by DNA microarray analyses using HG-U133 plus 2.0 oligonucleotide array. Partial array data on selected gene products were confirmed by RT-PCR and Western blotting. Ingenuity Pathway Analysis (IPA) was used to identify functional subsets of genes and biologically significant network pathways. 6-MTITC showed the highest number of differentially altered (≥2 folds) gene expression, of which 114 genes were upregulated and 75 were downregulated. IPA revealed that Nrf2-mediated pathway, together with glutamate metabolism, is the common significantly modulated pathway across treatments. Interestingly, 6-MSITC exhibited the most potent effect toward Nrf2-mediated pathway. Our data suggest that 6-MSITC could exert chemopreventive role against cancer through its underlying antioxidant activity via the activation of Nrf2-mediated subsequent induction of cytoprotective genes. [ABSTRACT FROM PUBLISHER]

Objective: This study aimed to explore the mechanism of p47phox-induced increase of reactive oxygen species (ROS) in peripheral blood mononuclear cells (PBMCs) from premature infants after oxygen therapy, and determine a new target for oxidative stress injury alleviation in clinical setting.Methods: First, ROS levels as well as p47phox translocation and expression in PBMC samples were evaluated after treatment of premature infants with different concentrations of oxygen. Then, changes of all various parameters were detected after in vitro treatment of PBMCs with diphenyleneiodonium (DPI), apocynin, and high oxygen levels.Results: In premature infants, ROS levels increased significantly after treatment with oxygen, in a concentration-dependent manner (p < 0.05); meanwhile, p47phox translocation and expression were significantly enhanced (p < 0.05) as well. In agreement, PBMCs cultured in vitro showed increased ROS levels after treatment with high oxygen concentrations; p47phox translocation, and expression increased as well (p < 0.05). However, treatment with DPI or apocynin resulted in opposite effects.Conclusion: Treatment with oxygen increases p47phox translocationand expression, which in turn induce ROS production. DPI and apocynin have the opposite effects. [ABSTRACT FROM AUTHOR]

Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods. [ABSTRACT FROM AUTHOR]

Conclusion The present findings show that all four types of histamine receptors (H1R, H2R, H3R, and H4R) are present in the inner ear, thus supporting the hypothesis that histamine plays a physiological role in the inner ear. Objective To analyse the presence of histamine receptors in the normal mouse inner ear. Methods CBA/J mice were used in this study. The localization of H1R, H2R, H3R, and H4R in the inner ear, i.e. cochlea, vestibular end organs, vestibular ganglion, and endolymphatic sac, was studied by real-time PCR and immunohistochemistry. Results The mRNA for each receptor sub-type was detected in the inner ear. In the immunohistochemical study, the organ of Corti, spiral ganglion, vestibular ganglion, vestibular sensory epithelium, and endolymphatic sac cells showed an immunofluorescent reaction to all histamine receptors. [ABSTRACT FROM AUTHOR]

Objectives: To identify the differences and similarities of differentially expressed genes in peripheral blood mononuclear cells (PBMCs) between Kashin-Beck disease (KBD) grades I and II.Method: In total, 100 patients with KBD and 100 healthy controls were selected from a KBD endemic area and divided into 100 pairs of KBD vs. controls (50 pairs of patients with KBD grade I and healthy controls, 50 pairs of patients with KBD grade II and healthy controls). RNA was isolated from KBD PBMCs and healthy control PBMCs. Microarray analysis was conducted to identify differentially expressed genes in the different stages of KBD. The microarray data obtained were further confirmed using quantitative real-time polymerase chain reaction (qRT-PCR).Results: In total, eight differentially expressed genes in KBD grade I and 69 differentially expressed genes in KBD grade II were identified. Among these genes, six common genes were differentially expressed in both stages of the disease. The expression ratios of four common genes differed significantly between KBD grades I and II. Based on the expression ratios of the four genes, linear discriminant analysis (LDA) correctly classified the KBD grade (I or II) with 81% accuracy.Conclusions: The similarities and differences of differentially expressed genes in PBMCs of patients with different stages of KBD may play an important role in the pathogenesis of the early phase of KBD. Additionally, six common genes may be considered blood-based genetic biomarkers for the detection and treatment of KBD. [ABSTRACT FROM AUTHOR]

Purpose: To assess the bacterial community structure and the possible mechanism underlying the environmental adaption in contaminated habitats.Methods: The 60-mer oligonucleotide multibacterial microarray (GSE38004) was downloaded from the Gene Expression Omnibus database. The changes in the abundance of bacterial populations and genes in contaminated habitats were assessed based on the gene expression profiles. Then the potential function of the genes and their involved pathways were predicted by a bioinformatics approach.Results: A total of 25 bacterial populations had different abundance between contaminated habitats and uncontaminated area, of whichSphingobium herbicidovorans(S. herbicidovorans)andPseudomonas pavonaceae (P. pavonaceae)involved in 23 populations were determined to have higher abundance in contaminated areas. Additionally, 184 genes involved in anaerobic respiration and cellular respiration were detected to have potential bioremediation. The genes ofMDH(Mannitol-1-phosphate/altronate dehydrogenases) andfadE(acyl-CoA dehydrogenase) may play key roles in the mechanism of metabolic adaption.Conclusions:S. herbicidovoransandP. pavonaceaewere the predominant bacterial groups in contaminated sites for the various metabolic potential and antibiotic resistances. The significant genes (MDH, fadE) and pathways (citrate cycle, pyruvate metabolism, fatty acid metabolism) played key roles in the adaptive response of microorganisms in contaminated environment. [ABSTRACT FROM AUTHOR]

Objective: The gene expression of transforming growth factor beta-1 (TGF-β1) in human placental samples obtained from pregnancies with small for gestational age fetuses (SGA) was compared to those of normal pregnancies.Methods: In 2011 placental samples from 101 pregnancies with SGA and from 140 normal pregnancies were obtained for analysis of TGF-β1 gene expression. Several clinical parameters were also assessed for correlation between genetic and clinical parameters.Results: There were no significant differences in gene activity of the TGF-β1 gene between the SGA versus normal pregnancy groups (Ln2α: 0.16; p = 0.07). Within the SGA group, no fetal gender-dependent differences were seen in TGF-β1 gene expression (Ln2α: −0.11; p = 0.05). Similarly, no significant differences in gene activity were observed by the degree of severity of SGA as assessed by percentile fetal birth-weight (Ln2α: 0.32; p = 0.06).Conclusion: We found no change in gene expression of TGF-β1 in placental samples obtained from SGA pregnancies versus normal pregnancy suggesting an absence of a direct role of the TGF-β1 gene in the development of SGA. However, the absence of increased gene expression of TGF-β1 in SGA can be conceptualized as a failure to mount a compensatory response in the SGA environment. [ABSTRACT FROM AUTHOR]

Of more than 2 million segmental bone defects repaired annually with bone autografts and allografts, 15-40% fail. Improving healing rates may be approached with tissue engineering and use of periosteum overlying an allograft. The present study documents gene expression in human periosteum-allograft constructs compared to allografts alone. Strips of human cadaveric periosteum (26 years, f, distal femur) were sutured about sterilized human femoral cortical strut bone allograft (54 years, m) segments. After construct incubation (M199 supplemented medium) for 8 d, constructs and allografts alone were implanted in nude mice. At 10 and 20 weeks, constructs ( N = 4, each group) and allografts ( N = 2, each group) were retrieved and placed in RNAlater for quantitative PCR to determine expression of human- and murine-specific genes relevant to remodeling. Specimens were frozen-ground to powders and RNA was extracted, purified, reverse-transcribed, and amplified. Ribosomal protein (P0) was used to normalize sample quantities. Fold change plots were generated following statistical analyses comparing 20- to 10-week gene expression data. Allografts alone yielded no human-specific gene expression. Notable fold changes of human-specific alkaline phosphatase, bone sialoprotein, type I collagen, decorin, RANKL, RANK, cathepsin K, and osteocalcin in 20-week compared to 10-week specimens were found. Murine-specific expression of genes indicative of host mouse vascularization (RANK, type I collagen) was detected in both allograft alone and periosteum-allograft samples. Gene data confirm viable periosteum in constructs after 20 weeks. Relatively higher fold-change values of RANK, RANKL and cathepsin K indicate activities of osteoclast precursors, osteoclasts and osteoblasts involved in allograft remodeling during implantation. All additional genes of interest indicate osteoblast activity in new bone matrix formation. Gene data are directly correlated with previous and present histology work. The results of this study suggest that further investigations could help to establish whether autologous periosteum-allograft constructs could be used for the repair of bone defects. [ABSTRACT FROM AUTHOR]

Dentin matrix protein 1 (DMP1) is a key regulator of biomineralization within the extracellular matrix (ECM) of bone and plays a role in regulating osteogenic gene expression. Osteocalcin (OCN) is one of the most abundantly expressed non-collagenous proteins by osteoblasts. In the present study, we generated a mouse model (OC-DMP1) that overexpresses full-length DMP1 utilizing the mouse OCN promoter. Expression of genes encoding osteogenic transcription factors and ECM proteins during early post-natal development in male OC-DMP1 and wild type (WT) mice was evaluated in femurs and calvaria. Bones were dissected from n = 4 animals at 15, 30, 60 and 90-d of age. Total RNA was isolated, reverse transcribed, and real-time PCR analysis was performed. Results confirmed a difference ( p < 0.05) in osteogenic gene expression between OC-DMP1 and WT mice at the specified time points. Additionally, distinctive osteogenic gene expression profiles for calvaria and femur, representing intramembranous and endochondral bone formation, were identified. These data suggest that bone-specific DMP1 overexpression changes the pattern in osteogenic gene expression pattern thereby influencing bone development. This animal model presented here provides new opportunities for analysis of in vivo roles of DMP1 in bone. [ABSTRACT FROM AUTHOR]

Endogenous mobile genetic elements can give rise to de novo germline or somatic mutations that can have dramatic consequences for genome regulation both local and possibly more globally based on the site of integration. However if we consider them as "normal genetic" components of the reference genome then they are likely to modify local chromatin structure which would have an effect on gene regulation irrelevant of their ability to further transpose. As such they can be treated as any other domain involved in a gene × environment interaction. Similarly their evolutionary appearance in the reference genome would supply a driver for species specific responses/traits. Our recent data would suggest the hominid specific subset of retrotransposons, SINE-VNTR-Alu (SVA), can function as transcriptional regulatory domains both in vivo and in vitro when analyzed in reporter gene constructs. Of particular interest in the SVA element, were the variable number tandem repeat (VNTR) domains which as their name suggests can be polymorphic. We and others have previously shown that VNTRs can be both differential regulators and biomarkers of disease based on the genotype of the repeat. Here, we provide an overview of why polymorphism in the SVA elements, in particular the VNTRs, could alter gene expression patterns that could be mechanistically associated with different traits in evolution or disease progression in humans. [ABSTRACT FROM AUTHOR]

Premature ovarian failure (POF) contributes to amenorrhoea, infertility, early onset of menostasia and osteoporosis. This study profiled differentially expressed miRNAs for association with POF development. Ovarian tissue samples from 4-vinylcyclohexene diepoxide (VCD)-induced rat POF and normal rats were profiled for differentially expressed miRNAs using miRNA microarrays. A total of 63 miRNAs were up-regulated and 20 miRNAs were down-regulated in rat POF tissues versus the control tissues. qRT-PCR verified some of these altered miRNAs, i.e. miR-29a and miR-144 were down-regulated in POF tissues, which may target expression of PLA2G4A that is involved in prostaglandin biosynthesis, whereas miR-27b and miR-190 were up-regulated in POF tissues by negative control of PAPPA and CCL2 expression, respectively, both of which have been shown to relate to response to hormone stimulus. Moreover, the up-regulated miR-151 and miR-672 can also target expression of TNFSF10 and FNDC1, which have been shown to positively regulate cell apoptosis. Profiling of differentially expressed miRNAs in POF provided a novel insight into the molecular events involving the role of miRNAs in POF development with specific emphasis upon miR-27b, miR-190, miR-151, miR-672, miR-29a and miR-144. [ABSTRACT FROM AUTHOR]

The article presents a study which examines the the coexistence of clones in five patients with both forms of 13q14 interstitial deletion and deletion at the translocation breakpoint. Cytogenetic analyses were accomplished at the time of diagnosis in three patients. Disease progression was detected in two other patients. Cytogenetic analysis was performed on bone marrow or peripheral blood cells stimulated by oligonucleotide DSP30 and interleukin-2.

Background: Most Gram-negative community-acquired and nosocomial infections are caused by Escherichia coli and Klebsiella pneumoniae, among which increasing resistance due to extended-spectrum β-lactamase (ESBL) is a major problem. We present data from the first Danish nationwide prevalence study on ESBL-producing E. coli, K. pneumoniae, and Proteus mirabilis in blood and urine cultures from hospitals and the community. Methods: During September and October 2007, 13 of 15 Danish departments of clinical microbiology collected data and strains. Confirmatory ESBL test-positive isolates were sent to a central laboratory for species and ESBL-phenotype confirmation, extended susceptibility testing, phylogenetic grouping of E. coli strains, and ESBL gene characterization. Results: During the study, blood samples from 18,259 patients and urine samples from 47,504 patients were subjected to culture. Among 14,674 cultured isolates, 352 were confirmed to be ESBL-producers. Thus, the crude ESBL prevalence was 2.4% (range 1.5% of E. coli in community urine to 6.6% of K. pneumoniae in hospital urine). An average of 7.2 ESBL-producers per 100,000 consumed bed-days was calculated. Of the 352 reported ESBL-producers, 205 E. coli, 73 K. pneumoniae, and 1 P. mirabilis, were available for testing. CTX-M enzymes dominated, both in hospitals and in the community, occurring in 92% of E. coli and 88% of K. pneumoniae, and with CTX-M-15 constituting 60% and 77%, respectively. Conclusions: Compared to 2003 data the ESBL prevalence in Denmark has increased significantly. In the ESBL-producers, reduced susceptibility towards both gentamicin and ciprofloxacin was seen among 43% E. coli and 55% K. pneumoniae, leaving clinicians in these cases with only a carbapenem for the treatment of serious infections. Part of this study was presented at the 20th European Congress of Clinical Microbiology and Infectious Diseases, abstract P-1617. [ABSTRACT FROM AUTHOR]

Medicinal plants contain a wide variety of active principles that have been exploited for the treatment of various ailments by a majority of the world's population. In recent years, many advanced biotechnological methods are employed to select, multiply, improve, and analyze medicinal plants for their application in traditional and modern medicinal preparations and drug discovery. The purpose of the present review is to focus on the application of biotechnological tools for multiplication and genetic enhancement of the medicinal plants by adopting techniques including in vitro regeneration and genetic transformation and highlight selected approaches followed for drug discovery from medicinal plants. [ABSTRACT FROM AUTHOR]

Follicular lymphoma (FL) is characterized by an indolent and relapsing course. Recently, the clinical outcome of FL has been distinguished by immune microenvironment-associated gene signatures. In our study, gene expression profiling (GEP) was performed in 31 non-selected patients with follicular lymphoma (FL), 12 of whom were in relapse and the remaining 19 newly diagnosed. A custom oligonucleotide microarray (Agilent 8 × 15K) was used which contained probes for about 3500 genes, including those that had been previously published as demonstrating significant prognostic value. An unsupervised approach was not able to recognize clinically different FLs. As the previously published prognostically relevant gene signatures could not be properly verified, probably due to microarray platform differences, template matching was therefore used in order to define two gene sets with differential gene expression among our samples. These gene sets shared an overrepresentation of genes with similar biological functions and were termed 'T-CELL' and 'PROLIFERATION' profiles. The 'poor profile' was then defined by a high PROLIFERATION score (upper tertile) and/or low T-CELL score (lower tertile). The 'poor profile' cohort contained a significantly higher proportion of relapsed cases ( p < 0.05, Fisher's exact test). Additionally, a comparison of samples from initial diagnosis and from relapse showed significant differences mainly in the T-CELL profile ( p = 0.036; χ2). This supports the hypothesis that the number of T-cells and their expression pattern play a major role in FL development. [ABSTRACT FROM AUTHOR]

Nucleoside triphosphates having a 3'-ONH2 blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3'-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3'-ONH2 group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3'-ONH2 blocking group in 'next generation sequencing.' [ABSTRACT FROM AUTHOR]

Since the early 1970s, the use of nucleic acid sequences for specific diagnostic applications has followed a somewhat linear pattern of development. Early methods for restriction enzyme digestion, as well as reverse transcription, were followed in the late 1970s by Southern, northern and dot blotting, as well as DNA sequencing. In 1985, the description of PCR and the routine laboratory manipulation of sufficient quantities of DNA for diagnostics, resulted in the exponential growth of molecular biology. Subsequently, alternative DNA and RNA amplification protocols followed. The last 10 years have seen the second explosion in molecular biology with the development of real-time quantitative PCR and oligonucleotide microarrays. This advancement continues with the development of methods for 'direct' nucleic acid target detection from samples without in vitro amplification, and enhanced transduction elements for improved sensitivity of nucleic acid detection. In this article, we will describe the current state of the art in nucleic acid diagnostics, the use of nucleic acid-based diagnostics in clinical practice and the emerging technologies in the field. Finally, we will describe future trends and expected advances in the field. INSET: Key issues. [ABSTRACT FROM AUTHOR]

The article discusses the use of next generation sequencing (NGS) in addressing the adoptees' lack of access to their genetic-relative family health history (GRFHx) with reference to the article "Does Lack of 'Genetic-Relative Family Health History' Represent a Potentially Avoidable Health Disparity for Adoptees" by Thomas May and colleagues in the same issue. Topics covered include the limitations of using NGS in identifying pathogenic genes, variant classification, and variant interpretation.

The article presents a case study of a 48-year-old woman suffering from bilateral salpingo-oophorectomy, omentectomy in large right ovarian mass. Topics discussed include no detection of surface tumor, surgicopathological diagnosis of FIGO stage with benign and borderline areas, her genetic studies showing copy-number (CN) aberrations, and CN analysis of genome suggesting correlation of genetic changes with histopathology in benign and malignant ovarian tumour.

Malignant transformation is thought to be associated with changes in the expression of a number of genes, and this alteration in gene expression is felt to be critical to the development of the malignant phenotype. Sarcomas represent a diverse group of tumors derived from cells of mesenchymal origin. Marked heterogeneity exists in the biological behavior of sarcomas, even within histologic subtypes of sarcomas. In an effort to better understand the biology of liposarcomas, gene expression in normal adipose tissue, lipomas, and liposarcomas was examined using the Affymetrix microarray technology. Differences in gene expression were quantified as the fold change in gene expression among the sample sets. Differences in gene expression among normal adipose tissue, lipomas, and liposarcomas were observed. In addition, genes expressed uniquely in liposarcoma among these and 18 other tissue sample sets were identified. Gene sets were devised that allowed the separation of liposarcomas from other samples, and most normal adipose tissue from most lipomas using the Eisen clustering software "Cluster." We conclude that differences in gene expression can be identified among different tumors derived from the adipocyte series. Such differences in gene expression may help differentiate among subtypes of sarcomas, and may also yield clues to the pathophysiology of this heterogeneous group of tumors. [ABSTRACT FROM AUTHOR]

Focuses on the use of microarray technology in molecular phenotyping of the immune system. Generation of data for thousands of genes through the technology; Platforms used for microarray analysis; Use of domain software to analyze data for scanned arrays.

Over the past decade, testing the genes of patients and their specific cancer types has become standardized practice in medical oncology since somatic mutations, changes in gene expression and epigenetic modifications are all hallmarks of cancer. However, while cancer genetic assessment has been limited to single biomarkers to guide the use of therapies, improvements in nucleic acid sequencing technologies and implementation of different genome analysis tools have enabled clinicians to detect these genomic alterations and identify functional and disease-associated genomic variants. Next-generation sequencing (NGS) technologies have provided clues about therapeutic targets and genomic markers for novel clinical applications when standard therapy has failed. While Sanger sequencing, an accurate and sensitive approach, allows for the identification of potential novel variants, it is however limited by the single amplicon being interrogated. Similarly, quantitative and qualitative profiling of gene expression changes also represents a challenge for the cancer field. Both RT-PCR and microarrays are efficient approaches, but are limited to the genes present on the array or being assayed. This leaves vast swaths of the transcriptome, including non-coding RNAs and other features, unexplored. With the advent of the ability to collect and analyze genomic sequence data in a timely fashion and at an ever-decreasing cost, many of these limitations have been overcome and are being incorporated into cancer research and diagnostics giving patients and clinicians new hope for targeted and personalized treatment. Below we highlight the various applications of next-generation sequencing in precision cancer medicine. [ABSTRACT FROM PUBLISHER]

Editorial. Focuses on the use of microarrays analysis technology for molecular phenotyping of the immune system. Application of the technology in the working of the immune system in both normal and malignant conditions; Benefits of the technology; Implications of the technology.