Explore the vast range of titles available.

Low-density DNA microarrays are crucial in molecular diagnostics due to their cost-effectiveness and high sensitivity. However, reliable spot localization remains challenging due to positional variations and image artifacts. Traditional intensity-based methods often struggle with weak fluorescence signals. To address this, we propose a rapid spot localization method that combines template matching with point pattern matching, enhanced through vectorized programming and square (box) templates. Vectorized programming accelerated the most time-consuming calculation by 82 times on a PC and was 6000 times faster on a Raspberry Pi compared to a for-loop implementation. While this improvement applies to the vectorized square calculation alone, substantial performance gains were still achieved in the overall process. Additionally, replacing circular templates with square templates resulted in a fourfold reduction in processing time without compromising detection performance. The proposed method effectively reduces computational overhead, making it suitable for high-throughput and resource-constrained applications. The method was validated using HPV genotyping images from commercial DNA microarrays, demonstrating its practical applicability and robust performance in clinical settings.

Microorganisms are the most diverse group of organisms and play important and distinctive roles in their ecosystems. They interact with their peers and other organisms (e.g., plants, animals) to form a complicated food web, significantly impacting ecosystem functions and services. However, understanding the diversity, composition, structure, function, activity, and dynamics of microbial communities remains challenging. Over the past decade, microarray-based technologies have been developed to address such challenges. This book is focused on current microarray technologies and their applications in environmental microbiology. In the first chapter, microarray technologies and applications are briefly introduced and, in following chapters, microarray probe design, development and evaluation, and data analysis are described in detail. In later chapters, more attention is paid to phylogenetic arrays (e.g., PhyloChip) and functional gene arrays (e.g., GeoChip). These generic tools - for analyzing microbial communities from disparate environments, ecosystems, and habitats (including soil, water, sediment, animals, and humans) - are described in detail with examples of specific applications. Also included are microarrays for analyzing microbial communities from specific environments, such as soil, bioleaching ecosystems, and human microbiomes, as well as microarrays for detecting specific microorganisms (e.g., pathogens) in the environment. The book's contributors also discuss the advantages and limitations of microarray technologies compared to high throughput sequencing technologies. This book is recommended for anyone working on microbial communities, biofilms, or environmental microbiology.

Background China has a high burden of Mycobacterium tuberculosis (MTB), with increasing infections from non-tuberculous mycobacteria (NTM). Rapid and accurate identification is crucial for effective clinical management. This study aimed to evaluate the diagnostic performance of DNA microarray chip and identify risk factors associated to mycobacterial infections. Methods Between January 2021 and June 2023, 973 patients with presumptive mycobacterial infections were recruited from the First Affiliated Hospital of Guangzhou Medical University. Various detection methods were used for etiological diagnosis, and their performance was compared. Multivariable logistic regression analysis determined clinical risk factors for mycobacterial positivity. Results Mycobacterial infection was confirmed in 438 patients, with 254 (58.0%) infected with MTB, 183 (41.8%) with NTM, and one co-infected with two. DNA microarray chip demonstrated the highest true positive rate (TPR) for mycobacterial detection at 96.8% and a true negative rate (TNR) of 90.8%. For MTB, the TPR was 94.5% with a TNR of 99.3%. Risk factors included cough/expectoration, pulmonary consolidation, cavitation, and bronchiectasis for mycobacterial infection, while smoking history and diabetes mellitus were independent risk factors for MTB infection. Conclusions DNA microarray chip offers a sensitive and specific diagnostic approach for mycobacterial infections, potentially enhancing clinical diagnosis and informing targeted interventions.

In recent years, exploring natural compounds with functional properties to ameliorate aging-associated cognitive decline has become a research priority to ensure healthy aging. In the present study, we investigated the effects of Trigonelline (TG), a plant alkaloid, on memory and spatial learning in 16-week-old senescence-accelerated mouse model SAMP8 using an integrated approach for cognitive and molecular biology aspects. After 30 days of oral administration of TG at the dose of 5 mg/kg/day, the mice were trained in Morris Water Maze task. TG-treated SAMP8 mice exhibited significant improvement in the parameters of escape latency, distance moved, and annulus crossing index. Next, we performed a whole-genome transcriptome profiling of the mouse hippocampus using microarrays. Gene ontology analyses showed that a wide range of biological processes, including nervous system development, mitochondrial function, ATP synthesis, and several signaling pathways related to inflammation, autophagy, and neurotransmitter release, were significantly enriched in TG-treated SAMP8 compared to nontreated. Further, a nonlinear dimensionality reduction technique, Uniform Manifold Approximation and Projection (UMAP), was applied to identify clusters of functions that revealed TG primarily regulated pathways related to inflammation, followed by those involved in neurotransmitter release. In addition, a protein–protein interaction network analysis indicated that TG may exert its biological effects through negatively modulating Traf6-mediated NF-κB activation. Finally, ELISA test showed that TG treatment significantly decreased proinflammatory cytokines- TNFα and IL6 and increased neurotransmitters- dopamine, noradrenaline, and serotonin in mouse hippocampus. Altogether, our integrated bio-cognitive approach highlights the potential of TG in alleviating age-related memory and spatial impairment.

Background Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays’ probe design cannot fully consider the vast human genetic diversity, leading to genetic artifacts. Distinguishing genuine from artifactual genetic influence is of particular relevance in the study of DNA methylation heritability and methylation quantitative trait loci. But despite its importance, current strategies to account for genetic artifacts are lagging due to a limited mechanistic understanding on how such artifacts operate. Results To address this, we develop and benchmark UMtools, an R-package containing novel methods for the quantification and qualification of genetic artifacts based on fluorescence intensity signals. With our approach, we model and validate known SNPs/indels on a genetically controlled dataset of monozygotic twins, and we estimate minor allele frequency from DNA methylation data and empirically detect variants not included in dbSNP. Moreover, we identify examples where genetic artifacts interact with each other or with imprinting, X-inactivation, or tissue-specific regulation. Finally, we propose a novel strategy based on co-methylation that can discern between genetic artifacts and genuine genomic influence. Conclusions We provide an atlas to navigate through the huge diversity of genetic artifacts encountered on DNA methylation microarrays. Overall, our study sets the ground for a paradigm shift in the study of the genetic component of epigenetic variation in DNA methylation microarrays.

Background: Diabetic nephropathy (DN) is a serious condition that can result in end-stage renal failure. Recent evidence has focused on the dietary effects of polyphenols on blood glucose levels and the complications of diabetes. Objectives: In this study, we investigated the protective effect of glucosyl hesperidin (G-Hes), composed of glucose and hesperidin, against streptozotocin (STZ)-induced nephropathy in mice. Methods: We used an STZ-induced diabetic mouse model to investigate the preventive effect of G-Hes on renal pathology. After G-Hes supplementation for 4 weeks, we investigated the renal gene expression profiles using DNA microarray analysis and renal histology to examine the underlying molecular mechanism. Results: G-Hes suppressed the increase in kidney weight without any change in the blood glucose levels. This study identified 511 genes whose expression levels were substantially increased during DN development but were downregulated by G-Hes supplementation. G-Hes prevented mRNA expression associated with renal tubule injury, fibrosis, and immune responses. Notably, G-Hes supplementation considerably decreased the complement component C3 at the mRNA and protein levels in the glomeruli and ameliorated glomerular and mesangial matrix expansion in diabetic nephropathy. Conclusions: G-Hes supplementation is useful in preventing tubulointerstitial fibrosis and inflammation in a mouse model of DN, without exhibiting a hypoglycemic effect.

The raccoon dog (Nyctereutes procyonoides) is known to be an opportunistic generalist who feeds on a wide variety of foods. Historically, their diet has been investigated by morphological observation of undigested remains in feces, requiring specialized knowledge such as osteology, zoology, and phytology. Here, we used DNA metabarcoding of vertebrate 12S rRNA gene and invertebrate 16S rRNA gene to investigate their fecal contents. Additionally, we developed a blocking oligonucleotide that specifically inhibits the amplification of the canid 12S rRNA gene. We confirmed that the blocking oligonucleotide selectively inhibit the amplification of raccoon dog's DNA without significantly changing the composition of the preys' DNA. We found that the main foods of raccoon dogs in our study area, the waterside of paddy fields in Korea, were fishes such as Cyprinidae and insects such as mole crickets, which makes sense given the Korean fauna and their well-known opportunistic feeding behaviors. As a method to conveniently and objectively investigate feeding habits of raccoon dogs, this study provided baseline information on DNA metabarcoding. By using DNA metabarcoding, it is expected that the diet habits and ecology of raccoon dogs will be better understood by future research.

Protein malnutrition promotes hepatic steatosis, decreases insulin-like growth factor (IGF)-I production and retards growth. To identify new molecules involved in such changes, we conducted DNA microarray analysis on liver samples from rats fed an isoenergetic low-protein diet for 8 h. We identified the fibroblast growth factor 21 gene (Fgf21) as one of the most strongly up-regulated genes under conditions of acute protein malnutrition (P<0·05, false-discovery rate<0·001). In addition, amino acid deprivation increased Fgf21 mRNA levels in rat liver-derived RL-34 cells (P<0·01). These results suggested that amino acid limitation directly increases Fgf21 expression. FGF21 is a polypeptide hormone that regulates glucose and lipid metabolism. FGF21 also promotes a growth hormone-resistance state and suppresses IGF-I in transgenic mice. Therefore, to determine further whether Fgf21 up-regulation causes hepatic steatosis and growth retardation after IGF-I decrease in protein malnutrition, we fed an isoenergetic low-protein diet to Fgf21-knockout (KO) mice. Fgf21-KO did not rescue growth retardation and reduced plasma IGF-I concentration in these mice. Fgf21-KO mice showed greater epididymal white adipose tissue weight and increased hepatic TAG and cholesterol levels under protein malnutrition conditions (P<0·05). Overall, the results showed that protein deprivation directly increased Fgf21 expression. However, growth retardation and decreased IGF-I were not mediated by increased FGF21 expression in protein malnutrition. Furthermore, FGF21 up-regulation rather appears to have a protective effect against obesity and hepatic steatosis in protein-malnourished animals.

[This corrects the article DOI: 10.1371/journal.pone.0259518.].

Objective and design To investigate whether di-(2-ethylhexyl) phthalate (DEHP) affects the production of inflammatory cytokines by human macrophages. Materials and methods Differentiated macrophage-like THP-1 cells were exposed to 200 μM DEHP for 3 h, followed by incubation in the presence or absence of opsonized zymosan A, and the concentrations of TNF-α, IL-1β, IL-8, and IL-6 in the culture media were determined by ELISA. DNA microarray and quantitative real-time RT-PCR analyses were performed to identify genes that showed changes in expression in response to DEHP. Results DEHP treatment increased the concentrations of TNF-α, IL-1β, IL-8, and IL-6 in the media, regardless of whether the cells phagocytosed zymosan. DNA microarray analysis showed that DEHP increased the levels of expression of IL-8, CXCL1, CXCL2, CXCL3, CXCL6, CCL3, MMP3, MMP10, MMP14, and CSF2 mRNA, and real-time RT-PCR showed that DEHP significantly enhanced the levels of expression of IL-8, CXCL1, CXCL2, CXCL3, CXCL6, CCL3, MMP10, CSF2, TNF-α, IL-1β, and IL-6 mRNA in THP-1 cells. DEHP significantly induced translocation of p65 NF-κB into the nucleus. Conclusion DEHP enhances the production of inflammatory cytokines and chemokines by macrophages, and exacerbates their inflammatory response.