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Background: The Csangos are an East-Central European ethnographic group living mainly in east of Transylvania in Romania. Traditionally, ethnography distinguishes three Csango subpopulations, the Moldavian, Gyimes and Burzenland Csangos. In our previous study we found that the Moldavian Csangos have East Asian/Siberian Turkic ancestry components that might be unique in the East-Central European region and might help to better understand the history of Hungarian speaking ethnic groups of the area. Since then, we obtained further Csango samples from Moldavia and from a distinct region of Gyimes, which two Csango subgroups are traditionally different since they live in a degree of isolation not only from other people but also from each other. Here we present the first genomic analysis of Gyimes Csangos, which intended to compare the genetic makeup of these two Csango subgroups using both allele-frequency and haplotype-based methods. The main goal of the study was to investigate the genetic isolation of the Csangos on a genome-wide SNP basis and to assess the isolation of Gyimes Csangos, which in contrast to the Moldavians was not yet studied. Results: Our results show that these two Csango groups show slight differences from each other. We confirmed the genetic isolation of Moldavian Csangos and revealed that Gyimes Csangos have a similar, but detectably weaker isolation. In the case of Gyimes Csangos we detected also a stronger East European or presumably Asian derived ancestry. Conclusion: The Gyimes Csangos show a degree of genetic isolation comparable to that of the Moldavians. The Asian ancestry that differentiates the Moldavian Csango people from the other East-Central European populations may be present in the Gyimes Csangos in an even higher degree, since Gyimes Csango individuals show a more significant share from that ancestry component. [ABSTRACT FROM AUTHOR]

Leukemia is a form of cancer that affects the bone marrow and lymphatic system, and it requires complex treatment strategies that vary with each subtype. Due to the subtle morphological differences among these types, monitoring gene expressions is crucial for accurate classification. Manual or pathological testing can be time-consuming and expensive. Therefore, data-driven methods and machine learning algorithms offer an efficient alternative for leukemia classification. This study introduced a novel super learning model that leverages heterogeneous machine learning models to analyze gene expression data and classify leukemia cells. The proposed approach incorporates an entropy-based feature importance technique to identify the gene profiles most significant to the labeling process. The strength of this super learning model lies in its final super learner, Random Forest, which effectively classifies cross-validated data from the candidate learners. Validation on a gene expression monitoring dataset demonstrates that this model outperforms other state-of-the-art models in predictive accuracy. The study contributes to the knowledge regarding the use of advanced machine learning techniques to improve the accuracy and reliability of leukemia classification using gene expression data, addressing the challenges of traditional methods that rely on clinical features and morphological examination. [ABSTRACT FROM AUTHOR]

DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects. [ABSTRACT FROM AUTHOR]

Abstract Background The Csangos are an East-Central European ethnographic group living mainly in east of Transylvania in Romania. Traditionally, ethnography distinguishes three Csango subpopulations, the Moldavian, Gyimes and Burzenland Csangos. In our previous study we found that the Moldavian Csangos have East Asian/Siberian Turkic ancestry components that might be unique in the East-Central European region and might help to better understand the history of Hungarian speaking ethnic groups of the area. Since then, we obtained further Csango samples from Moldavia and from a distinct region of Gyimes, which two Csango subgroups are traditionally different since they live in a degree of isolation not only from other people but also from each other. Here we present the first genomic analysis of Gyimes Csangos, which intended to compare the genetic makeup of these two Csango subgroups using both allele-frequency and haplotype-based methods. The main goal of the study was to investigate the genetic isolation of the Csangos on a genome-wide SNP basis and to assess the isolation of Gyimes Csangos, which in contrast to the Moldavians was not yet studied. Results Our results show that these two Csango groups show slight differences from each other. We confirmed the genetic isolation of Moldavian Csangos and revealed that Gyimes Csangos have a similar, but detectably weaker isolation. In the case of Gyimes Csangos we detected also a stronger East European or presumably Asian derived ancestry. Conclusion The Gyimes Csangos show a degree of genetic isolation comparable to that of the Moldavians. The Asian ancestry that differentiates the Moldavian Csango people from the other East-Central European populations may be present in the Gyimes Csangos in an even higher degree, since Gyimes Csango individuals show a more significant share from that ancestry component.

Abstract Leukemia is a form of cancer that affects the bone marrow and lymphatic system, and it requires complex treatment strategies that vary with each subtype. Due to the subtle morphological differences among these types, monitoring gene expressions is crucial for accurate classification. Manual or pathological testing can be time-consuming and expensive. Therefore, data-driven methods and machine learning algorithms offer an efficient alternative for leukemia classification. This study introduced a novel super learning model that leverages heterogeneous machine learning models to analyze gene expression data and classify leukemia cells. The proposed approach incorporates an entropy-based feature importance technique to identify the gene profiles most significant to the labeling process. The strength of this super learning model lies in its final super learner, Random Forest, which effectively classifies cross-validated data from the candidate learners. Validation on a gene expression monitoring dataset demonstrates that this model outperforms other state-of-the-art models in predictive accuracy. The study contributes to the knowledge regarding the use of advanced machine learning techniques to improve the accuracy and reliability of leukemia classification using gene expression data, addressing the challenges of traditional methods that rely on clinical features and morphological examination.

Background: Staphylococcus aureus is an important pathogen that causes mild to invasive infections in hospitals and the community. Although methicillinsusceptible Staphylococcus aureus (MSSA) isolates continue to cause different infections, there is no data on the genetic backgrounds of the MSSA colonizing or causing infections in Kuwait hospitals. This study aimed to investigate MSSA isolated from patients admitted to Kuwait hospitals for antibiotic resistance and genetic backgrounds to understand their clonal composition. Methods: Consecutive MSSA isolates were collected from single patients during two surveillance periods in 2016 and 2021 in 13 public hospitals. The isolates were characterized using antibiogram, staphylococcal protein A (spa) typing, DNA microarray analysis, and multilocus sequence typing (MLST) using standard protocols. Results: A total of 446 MSSA was cultured from different clinical samples in 2016 (n = 240) and 2021 (n = 206). All isolates were susceptible to vancomycin [minimum inhibitory concentration (MIC) ≤ 2 mg/L], teicoplanin (MIC ≤2 mg/L), linezolid (MIC ≤4 mg/L), ceftaroline (MIC ≤2 mg/L), rifampicin, and mupirocin but were resistant to erythromycin (21.3%), clindamycin (14.0%), gentamicin (3.8%), kanamycin (10.5%), fusidic acid (27.0%), tetracycline (6.9%), trimethoprim (23.1%), and ciprofloxacin (35.2%). Molecular typing identified 155 spa types, dominated by t127 (15.0%), t084 (5.4%), t3841 (5.4%), t267 (2.4%), t442 (2.2%), t091 (2.2%), t021 (2.2%), and t003 (2.2%); 31 clonal complexes (CCs); and 56 sequence types (STs). The majority of the isolates (n = 265; 59.4%) belonged to CC1 (20.6%), CC15 (10.9%), CC22 (5.1%), CC30 (7.6%), CC361 (10.1%), and CC398 (4.7%). Discussion: The MSSA isolates belonged to diverse genetic backgrounds dominated by CC1, CC15, CC22, CC30, CC361, and CC398. The distribution of MSSA clones in 2016 and 2021 showed the stability of these clones over time. The study provides the first comprehensive data on the clonal distribution of MSSA in Kuwait hospitals. [ABSTRACT FROM AUTHOR]

Seborrheic keratosis (SK) is a common benign tumour, often associated with hyperpigmentation. To investigate the mechanism of melanin accumulation in SK, we have conducted comprehensive gene expression and histological analyses. We obtained five pairs of skin samples, including non‐lesional and SK samples, from the backs of three male Japanese participants aged 40–59 years. To examine melanocytes and keratinocytes in SK, three pairs of skin samples were separated by laser capture microdissection into the basal layer and the other layer in the epidermis. We performed a comprehensive gene expression analysis to identify differentially expressed genes between non‐lesional and SK skin, followed by gene ontology and pathway analysis. We found abnormal morphogenesis and cell proliferation in the basal layer, along with increased immune response and impaired cell differentiation and metabolism in the other layer of SK. We focused on cell proliferation and differentiation, as these are directly associated with melanin accumulation. Immunohistochemical analyses of Ki67, keratin 10, and keratin 14 demonstrated the decreases in the proliferation and early differentiation of the epidermis. Contrarily, no significant changes were observed in terminal differentiation markers, filaggrin and loricrin. Although the number of melanocytes was higher in SK than in non‐lesional skin, melanogenic activity showed no difference. These results indicated that melanin accumulation in SK is caused by delayed melanin excretion due to reduced turnover around the basal and spinous layers of the epidermis and melanin production due to an increased number of melanocytes. Our findings provide new insights for therapeutic approaches in SK. [ABSTRACT FROM AUTHOR]

Much research has been conducted to determine how hair regeneration is regulated, as this could provide therapeutic, cosmetic, and even psychological interventions for hair loss. The current study focused on the hair growth effect and effective utilization of fatty oil obtained from Bryde's whales through a high-throughput DNA microarray approach in conjunction with immunohistochemical observations. The research also examined the mechanisms and factors involved in hair growth. In an experiment using female C57BL/6J mice, the vehicle control group (VC: propylene glycol: ethanol: water), the positive control group (MXD: 3% minoxidil), and the experimental group (WO: 20% whale oil) were topically applied to the dorsal skin of the mouse. The results showed that 3% MXD and 20% WO were more effective than VC in promoting hair growth, especially 20% WO. Furthermore, in hematoxylin and eosin-stained dorsal skin tissue, an increase in the number of hair follicles and subcutaneous tissue thickness was observed with 20% WO. Whole-genome transcriptome analysis also confirmed increases for 20% WO in filaggrin (Flg), a gene related to skin barrier function; fibroblast growth factor 21 (Fgf21), which is involved in hair follicle development; and cysteine-rich secretory protein 1 (Crisp1), a candidate gene for alopecia areata. Furthermore, the results of KEGG pathway analysis indicated that 20% WO may have lower stress and inflammatory responses than 3% MXD. Therefore, WO is expected to be a safe hair growth agent. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Advancements in genomic technologies have paved the way for significant breakthroughs in cancer diagnostics, with DNA microarray technology standing at the forefront of identifying genetic expressions associated with various cancer types. Despite its potential, the vast dimensionality of microarray data presents a formidable challenge, necessitating efficient dimension reduction and gene selection methods to accurately identify cancerous tumors. In response to this challenge, this study introduces an innovative strategy for microarray data dimension reduction and crucial gene set selection, aiming to enhance the accuracy of cancerous tumor identification. Leveraging DNA microarray technology, our method focuses on pinpointing significant genes implicated in tumor development, aiding the development of sophisticated computerized diagnostic tools. Our technique synergizes gene selection with classifier training within a logistic regression framework, utilizing a generalized Fused LASSO (GFLASSO-LR) regularizer. This regularization incorporates two penalties: one for selecting pertinent genes and another for emphasizing adjacent genes of importance to the target class, thus achieving an optimal trade-off between gene relevance and redundancy. The optimization challenge posed by our approach is tackled using a sub-gradient algorithm, designed to meet specific convergence prerequisites. We establish that our algorithm's objective function is convex, Lipschitz continuous, and possesses a global minimum, ensuring reliability in the gene selection process. A numerical evaluation of the method's parameters further substantiates its effectiveness. Experimental outcomes affirm the GFLASSO-LR methodology's high efficiency in processing high-dimensional microarray data for cancer classification. It effectively identifies compact gene subsets, significantly enhancing classification performance and demonstrating its potential as a powerful tool in cancer research and diagnostics. [ABSTRACT FROM AUTHOR]

Glutathione (GSH) has long been recognised for its antioxidant and detoxifying effects on the liver. The hepatoprotective effect of GSH involves the activation of antioxidative systems such as NRF2; however, details of the mechanisms remain limited. A comparative analysis of the biological events regulated by GSH under physiological and oxidative stress conditions has also not been reported. In this study, DNA microarray analysis was performed with four experiment arms including Control, GSH, hydrogen peroxide (HP), and GSH + HP treatment groups. The GSH-treated group exhibited a significant upregulation of genes clustered in cell proliferation, growth, and differentiation, particularly those related to MAPK, when compared with the Control group. Additionally, liver functions such as alcohol and cholesterol metabolic processes were significantly upregulated. On the other hand, in the HP-induced oxidative stress condition, GSH (GSH + HP group) demonstrated a significant activation of cell proliferation, cell cycle, and various signalling pathways (including TGFβ, MAPK, PI3K/AKT, and HIF-1) in comparison to the HP group. Furthermore, several disease-related pathways, such as chemical carcinogenesis–reactive oxygen species and fibrosis, were significantly downregulated in the GSH + HP group compared to the HP group. Collectively, our study provides a comprehensive analysis of the effects of GSH under both physiological and oxidative stress conditions. Our study provides essential insights to direct the utilisation of GSH as a supplement in the management of conditions associated with oxidative stress. [ABSTRACT FROM AUTHOR]

BackgroundStaphylococcus aureus is an important pathogen that causes mild to invasive infections in hospitals and the community. Although methicillin-susceptible Staphylococcus aureus (MSSA) isolates continue to cause different infections, there is no data on the genetic backgrounds of the MSSA colonizing or causing infections in Kuwait hospitals. This study aimed to investigate MSSA isolated from patients admitted to Kuwait hospitals for antibiotic resistance and genetic backgrounds to understand their clonal composition.MethodsConsecutive MSSA isolates were collected from single patients during two surveillance periods in 2016 and 2021 in 13 public hospitals. The isolates were characterized using antibiogram, staphylococcal protein A (spa) typing, DNA microarray analysis, and multilocus sequence typing (MLST) using standard protocols.ResultsA total of 446 MSSA was cultured from different clinical samples in 2016 (n = 240) and 2021 (n = 206). All isolates were susceptible to vancomycin [minimum inhibitory concentration (MIC) ≤ 2 mg/L], teicoplanin (MIC ≤2 mg/L), linezolid (MIC ≤4 mg/L), ceftaroline (MIC ≤2 mg/L), rifampicin, and mupirocin but were resistant to erythromycin (21.3%), clindamycin (14.0%), gentamicin (3.8%), kanamycin (10.5%), fusidic acid (27.0%), tetracycline (6.9%), trimethoprim (23.1%), and ciprofloxacin (35.2%). Molecular typing identified 155 spa types, dominated by t127 (15.0%), t084 (5.4%), t3841 (5.4%), t267 (2.4%), t442 (2.2%), t091 (2.2%), t021 (2.2%), and t003 (2.2%); 31 clonal complexes (CCs); and 56 sequence types (STs). The majority of the isolates (n = 265; 59.4%) belonged to CC1 (20.6%), CC15 (10.9%), CC22 (5.1%), CC30 (7.6%), CC361 (10.1%), and CC398 (4.7%).DiscussionThe MSSA isolates belonged to diverse genetic backgrounds dominated by CC1, CC15, CC22, CC30, CC361, and CC398. The distribution of MSSA clones in 2016 and 2021 showed the stability of these clones over time. The study provides the first comprehensive data on the clonal distribution of MSSA in Kuwait hospitals.

In this article, a new method is employed for maximizing the performance of the Least Absolute Shrinkage and Selection Operator (Lasso) feature selection model. In fact, we presented a novel regularization for the Lasso by employing an approach to find the best regularization parameter automatically which guarantees best performance of the Lasso in DNA microarray data classification. In our experiment, four well-known publicly available microarray datasets including breast cancer, Diffuse Large B-cell Lymphoma (DLBCL), leukemia and prostate cancer were utilized for evaluation the proposed methods. Experimental results demonstrated the significant dominance of the proposed Lasso against other widely used feature selection methods in terms of best features that led to best performance, robustness and stability in microarray data classification. Accordingly, the proposed method is a powerful algorithm for selection of most informative features which can be used for cancer diagnosis by gene expression profiles. [ABSTRACT FROM AUTHOR]

This article, published in the Austral Journal of Veterinary Sciences, discusses a study on the effects of selenium on gene expression in in vitro follicles of ewes. The study found that selenium activated gene expression in the follicles, particularly genes related to the immune system. The researchers identified numerous differentially expressed genes, some of which were involved in apoptosis regulation. The study suggests that selenium treatment affects the transcriptome and has implications for immune processes in ovarian follicles. Additionally, a list of references to related scientific articles is provided, covering topics such as biological trace elements, CD4(+) T cells, ovarian granulosa cell death, selenium, and immune responses. [Extracted from the article]

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen that causes serious infections in healthcare facilities and in communities. The purpose of this study was to investigate MRSA isolates obtained in a tertiary hospital in Kuwait to assess their antibiotic susceptibility profile and clonal composition. Sixty MRSA isolates collected in 2020 were tested through antibiotic susceptibility testing, spa typing, and DNA microarray analysis. All isolates were found to be susceptible to vancomycin (MIC: ≤3 µg/mL), teicoplanin (MIC: ≤3 µg/mL), rifampicin, and mupirocin, but were resistant to fusidic acid (n = 43, 72%), trimethoprim (n = 27, 45%), ciprofloxacin (n = 31, 51.7%), gentamicin (n = 14; 23.3%), kanamycin (n = 20; 33.3%), chloramphenicol (n = 7; 11.7%), tetracycline (n = 17; 28.3%), erythromycin (n = 19; 31.6%), inducible clindamycin (n = 13; 21.7%), and constitutive clindamycin (n = 2; 3.3%). The isolates belonged to 30 spa types and 13 clonal complexes (CCs). The dominant spa types were t304, t442, t311, t688, and t1234, collectively constituting 28.3% of the isolates. The dominant CCs were CC5 and CC6, which together constituted 46.7% of the isolates. This study provides updated research on antibiotic resistance and changes in the clonal composition of MRSA in a Kuwait hospital, including the disappearance of the ST239-MRSA-III clone that was previously the dominant clone in this hospital. [ABSTRACT FROM AUTHOR]

Zelalem Asmare,1 Mulat Erkihun2 1Department of Medical Laboratory Science, Woldia University, Woldia, Ethiopia; 2Department of Medical Laboratory Science, Debre Tabor University, Debre Tabor, EthiopiaCorrespondence: Zelalem Asmare, Email zelalemasmare018@gmail.comAbstract: Infectious diseases are considered a major cause of death globally, accounting for one-third of all deaths. Traditionally, microbiological approaches to diagnose infectious diseases have been labor-intensive and time-consuming; molecular methods significantly improve on these constraints. DNA microarray is a novel and advanced diagnostic test for infectious disease that is designed for specific identification of a wide variety of organisms simultaneously. Microarray has various advanced applications in infectious disease diagnostics, including the 2019 pandemic COVID 19, detection of food-borne infectious agents, and detection of Neisseria meningitidis. The aim of this review is to provide updated application of DNA microarray techniques for the diagnosis of infectious diseases and to explore the development of new DNA microarray methods. In conclusion, DNA microarray techniques are the future rapid and accurate diagnostic tool for infectious disease diagnosis and detection of antimicrobial resistance.Keywords: DNA microarray, infectious disease diagnostics, molecular techniques

Abstract Background Human papillomavirus (HPV) has been detected in eyelid sebaceous gland carcinoma (SGC) and squamous cell carcinoma (SCC), and detection rates greatly varied across studies. This study aimed to investigate the presence of HPV in eyelid SGC and SCC among Koreans and its correlation with clinicopathological characteristics. Methods Surgically resected eyelid samples diagnosed as SGC or SCC from January 1999 to June 2011 were identified from the pathology database of three referral centres in Korea. Clinicopathological information including origin (skin vs. tarsal conjunctiva) and treatment outcomes were retrospectively reviewed. Immunohistochemistry (IHC) for p16, HPV DNA in situ hybridisation (ISH), and polymerase chain reaction-based DNA microarray were performed in paraffin-embedded tissue sections. Results Our cohort included 34 SGC and 12 SCC cases with Asian ethnicity. HPV was detected in 4 SGC and 6 SCC by DNA microarray, while 2 SCC (16.7%) showed positivity in ISH. SCC of tarsal conjunctival origin was significantly more common in HPV-positive SCC than in HPV-negative SCC (5 of 6 vs. 0 of 6, P = 0.015, Fisher’s exact test). Among samples showing positive staining in p16 IHC, HPV positivity rates were 0.0% (0/19) in SGC and 100% (3/3) in SCC. There was no significant difference in overall and local recurrence rate in eyelid SGC and SCC according to the HPV status (P > 0.99). Conclusions HPV was found in a subset of eyelid SGC and SCC among Koreans and might be aetiologically related to SCC of tarsal conjunctival origin. Overexpression of p16 is considered to be inappropriate as an indicator of HPV infection in eyelid SGC. Further investigation is required to elucidate the transmission route and pathogenic roles of HPV.

Innate immunity is the organism's first line of defence, and the receptors of immune cells play a key role. Interleukin 1 receptor-associated kinase 1 and 4 (IRAK1 and IRAK4) are necessary for signal transmission from Toll-like receptors, which are the most important receptors of immune cells. The main objective of this study was to investigate the gene polymorphisms of IRAK1 and IRAK4 in Czech Fleckvieh cattle (CF) and to compare their diversity with other cattle breeds as there is still little information about these genes. PacBio Technology of next-generation sequencing (NGS) was used to detect genetic variability in 164 CF bulls. The results revealed 17 single nucleotide variants (SNVs) in the IRAK1 gene and 12 SNVs and three deletions in the IRAK4 gene. Three methods were then used to determine allelic variability: Sanger sequencing, the primer extension method and Illumina DNA BeadChip microarray in cooperation with the Czech Moravian Breeder's Corporation. Sanger sequencing enabled analysis of the population variability in single nucleotide polymorphisms (SNPs) rs210710958 and rs48726521 of IRAK1 in 164 CF bulls. SNaPshot genotyping was employed to determine the allelic frequencies of SNP rs211379365 and a novel polymorphism in IRAK1, and rs380202447 in the IRAK4 gene. DNA microarray method, which was applied to 74 CF dairy cows, revealed the allelic frequency of IRAK1 rs110533802 including the frequency 0.07 of mutant allele T. Additional microarray data allowed the comparison of the allelic frequencies among the Czech and Hungarian populations of Holstein dairy cows and beef breed populations. The results show that the functionally significant diversity in the IRAK1 and IRAK4 genes in the studied CF population is rather limited. The higher frequency 0.4 of the T mutant allele of SNP rs110533802 of IRAK1 in Holstein cattle could be the consequence of breeding for milk performance.

The aim of this research was to test the efficacy and potential clinical application of intranasal administration of galanin-like peptide (GALP) as an anti-obesity treatment under the hypothesis that GALP prevents obesity in mice fed a high-fat diet (HFD). Focusing on the mechanism of regulation of lipid metabolism in peripheral tissues via the autonomic nervous system, we confirmed that, compared with a control (saline), intranasally administered GALP prevented further body weight gain in diet-induced obesity (DIO) mice with continued access to an HFD. Using an omics-based approach, we identified several genes and metabolites in the liver tissue of DIO mice that were altered by the administration of intranasal GALP. We used whole-genome DNA microarray and metabolomics analyses to determine the anti-obesity effects of intranasal GALP in DIO mice fed an HFD. Transcriptomic profiling revealed the upregulation of flavin-containing dimethylaniline monooxygenase 3 (Fmo3), metallothionein 1 and 2 (Mt1 and Mt2, respectively), and the Aldh1a3, Defa3, and Defa20 genes. Analysis using the DAVID tool showed that intranasal GALP enhanced gene expression related to fatty acid elongation and unsaturated fatty acid synthesis and downregulated gene expression related to lipid and cholesterol synthesis, fat absorption, bile uptake, and excretion. Metabolite analysis revealed increased levels of coenzyme Q10 and oleoylethanolamide in the liver tissue, increased levels of deoxycholic acid (DCA) and taurocholic acid (TCA) in the bile acids, increased levels of taurochenodeoxycholic acid (TCDCA), and decreased levels of ursodeoxycholic acid (UDCA). In conclusion, intranasal GALP administration alleviated weight gain in obese mice fed an HFD via mechanisms involving antioxidant, anti-inflammatory, and fatty acid metabolism effects and genetic alterations. The gene expression data are publicly available at NCBI GSE243376. [ABSTRACT FROM AUTHOR]

Control of complex parasites via vaccination remains challenging, with the current combination of vaccines and small drugs remaining the choice for an integrated control strategy. Studies conducted to date, are providing evidence that multicomponent vaccines will be needed for the development of protective vaccines against endo- and ectoparasites, though multicomponent vaccines require an in-depth understanding of parasite biology which remains insufficient for ticks. With the rapid development and spread of acaricide resistance in ticks, new targets for acaricide development also remains to be identified, along with novel targets that can be exploited for the design of lead compounds. In this study, we analysed the differential gene expression of Rhipicephalus microplus ticks that were fed on cattle vaccinated with a multi-component vaccine (Bm86 and 3 putative Bm86-binding proteins). The data was scrutinised for the identification of vaccine targets, small drug targets and novel pathways that can be evaluated in future studies. Limitations associated with targeting novel proteins for vaccine and/or drug design is also discussed and placed into the context of challenges arising when targeting large protein families and intracellular localised proteins. Lastly, this study provide insight into how Bm86-based vaccines may reduce successful uptake and digestion of the bloodmeal and overall tick fecundity. [ABSTRACT FROM AUTHOR]

Background: Human papillomavirus (HPV) has been detected in eyelid sebaceous gland carcinoma (SGC) and squamous cell carcinoma (SCC), and detection rates greatly varied across studies. This study aimed to investigate the presence of HPV in eyelid SGC and SCC among Koreans and its correlation with clinicopathological characteristics. Methods: Surgically resected eyelid samples diagnosed as SGC or SCC from January 1999 to June 2011 were identified from the pathology database of three referral centres in Korea. Clinicopathological information including origin (skin vs. tarsal conjunctiva) and treatment outcomes were retrospectively reviewed. Immunohistochemistry (IHC) for p16, HPV DNA in situ hybridisation (ISH), and polymerase chain reaction-based DNA microarray were performed in paraffin-embedded tissue sections. Results: Our cohort included 34 SGC and 12 SCC cases with Asian ethnicity. HPV was detected in 4 SGC and 6 SCC by DNA microarray, while 2 SCC (16.7%) showed positivity in ISH. SCC of tarsal conjunctival origin was significantly more common in HPV-positive SCC than in HPV-negative SCC (5 of 6 vs. 0 of 6, P = 0.015, Fisher's exact test). Among samples showing positive staining in p16 IHC, HPV positivity rates were 0.0% (0/19) in SGC and 100% (3/3) in SCC. There was no significant difference in overall and local recurrence rate in eyelid SGC and SCC according to the HPV status (P > 0.99). Conclusions: HPV was found in a subset of eyelid SGC and SCC among Koreans and might be aetiologically related to SCC of tarsal conjunctival origin. Overexpression of p16 is considered to be inappropriate as an indicator of HPV infection in eyelid SGC. Further investigation is required to elucidate the transmission route and pathogenic roles of HPV. [ABSTRACT FROM AUTHOR]

Advancements in genomic technologies have paved the way for significant breakthroughs in cancer diagnostics, with DNA microarray technology standing at the forefront of identifying genetic expressions associated with various cancer types. Despite its potential, the vast dimensionality of microarray data presents a formidable challenge, necessitating efficient dimension reduction and gene selection methods to accurately identify cancerous tumors. In response to this challenge, this study introduces an innovative strategy for microarray data dimension reduction and crucial gene set selection, aiming to enhance the accuracy of cancerous tumor identification. Leveraging DNA microarray technology, our method focuses on pinpointing significant genes implicated in tumor development, aiding the development of sophisticated computerized diagnostic tools. Our technique synergizes gene selection with classifier training within a logistic regression framework, utilizing a generalized Fused LASSO (GFLASSO-LR) regularizer. This regularization incorporates two penalties: one for selecting pertinent genes and another for emphasizing adjacent genes of importance to the target class, thus achieving an optimal trade-off between gene relevance and redundancy. The optimization challenge posed by our approach is tackled using a sub-gradient algorithm, designed to meet specific convergence prerequisites. We establish that our algorithm’s objective function is convex, Lipschitz continuous, and possesses a global minimum, ensuring reliability in the gene selection process. A numerical evaluation of the method’s parameters further substantiates its effectiveness. Experimental outcomes affirm the GFLASSO-LR methodology’s high efficiency in processing high-dimensional microarray data for cancer classification. It effectively identifies compact gene subsets, significantly enhancing classification performance and demonstrating its potential as a powerful tool in cancer research and diagnostics.

The tumor suppressor p53 exerts its role mainly as a transcription factor. The TP53 gene, which encodes the p53 protein, is the most commonly mutated gene in human cancers, particularly triple negative breast cancer (TNBC). Variations in the TP53 gene occur mainly in exons 5–8 and result in missense mutations in the DNA-binding domain of the p53 protein that alter DNA binding specificity. To identify the target genes of mutant p53, we performed chromatin immunoprecipitation followed by DNA microarray (ChIP-chip). Briefly, the TNBC cell line MDA-MB-468 containing the endogenous p53-R273H mutation (the arginine residue at position 273 is mutated to a histidine) was cross-linked with 1% formaldehyde and ultrasonically sheared to generate chromatin fragments in a range of 200∼1000 bp. An aliquot of the sheared chromatin was kept as input, and the other chromatin was precipitated with a p53 monoclonal antibody. DNA was purified from the precipitated chromatin and the unprecipitated chromatin (i.e., input), amplified, and labeled with Cy5 (ChIP DNA) or Cy3 (input DNA). Cy5- and Cy3-labeled DNA samples were cohybridized with the NimbleGen Human ChIP-chip 2.1 M Deluxe Promoter Array. The raw and analyzed data are described in this article. They are useful for identifying target genes and consensus binding motifs of the p53 R273H mutant and for further clarifying the molecular mechanism underlying the oncogenic activity of the p53 mutant.

Objective: DNA microarray is a powerful method to identify genomic anomalies including small insertions, duplications and/or deletions. This method is widely used in routine genetic screening for explaining the genetic background of certain phenotypes, for example, cancer. Cell-free DNA (cfDNA), which is an approach that may give information about the somatic tissues in peripheral blood, is another popular method used in routine genetic screening to understand the background of particular phenotypes, one of which is cancer. There is limited available research that investigates the involvement of these two approaches to decipher novel cancer biomarkers in the literature. However, detection of cancer biomarkers, especially non-invasive types, has been of great interest to research groups. Materials and Methods: In the present study, we used colorectal cancer as a model tumor to figure out whether we could determine definite biomarkers from cfDNA using DNA microarray methodology. We isolated cfDNA from the cell-free mediums of the cultures of colorectal cancer cell lines in the presence of the control group which was the healthy epithelial colon cell line. Results: Our results underlined significant alterations that were deletions and/or duplications in some of the genomic regions in a cell line-specific manner. Conclusion: We propose that DNA microarray could be used to assess the sub-types of certain cancers in a non-invasive manner using cfDNA approaches. [ABSTRACT FROM AUTHOR]

Innate immunity is the organism’s first line of defence, and the receptors of immune cells play a key role. Interleukin 1 receptor-associated kinase 1 and 4 (IRAK1 and IRAK4) are necessary for signal transmission from Toll-like receptors, which are the most important receptors of immune cells. The main objective of this study was to investigate the gene polymorphisms of IRAK1 and IRAK4 in Czech Fleckvieh cattle (CF) and to compare their diversity with other cattle breeds as there is still little information about these genes. PacBio Technology of next-generation sequencing (NGS) was used to detect genetic variability in 164 CF bulls. The results revealed 17 single nucleotide variants (SNVs) in the IRAK1 gene and 12 SNVs and three deletions in the IRAK4 gene. Three methods were then used to determine allelic variability: Sanger sequencing, the primer extension method and Illumina DNA BeadChip microarray in cooperation with the Czech Moravian Breeder’s Corporation. Sanger sequencing enabled analysis of the population variability in single nucleotide polymorphisms (SNPs) rs210710958 and rs48726521 of IRAK1 in 164 CF bulls. SNaPshot genotyping was employed to determine the allelic frequencies of SNP rs211379365 and a novel polymorphism in IRAK1, and rs380202447 in the IRAK4 gene. DNA microarray method, which was applied to 74 CF dairy cows, revealed the allelic frequency of IRAK1 rs110533802 including the frequency 0.07 of mutant allele T. Additional microarray data allowed the comparison of the allelic frequencies among the Czech and Hungarian populations of Holstein dairy cows and beef breed populations. The results show that the functionally significant diversity in the IRAK1 and IRAK4 genes in the studied CF population is rather limited. The higher frequency 0.4 of the T mutant allele of SNP rs110533802 of IRAK1 in Holstein cattle could be the consequence of breeding for milk performance. [ABSTRACT FROM AUTHOR]

Abstract Next-generation RNA sequencing (RNA-Seq) has identified more differentially expressed protein-coding genes (DEGs) and provided a wider quantitative range of expression level changes than conventional DNA microarrays. JEMS·MMS·Toxicogenomics group studied DEGs with targeted RNA-Seq on freshly frozen rat liver tissues and on formalin-fixed paraffin-embedded (FFPE) rat liver tissues after 28 days of treatment with chemicals and quantitative real-time PCR (qPCR) on rat and mouse liver tissues after 4 to 48 h treatment with chemicals and analyzed by principal component analysis (PCA) as statics. Analysis of rat public DNA microarray data (Open TG-GATEs) was also performed. In total, 35 chemicals were analyzed [15 genotoxic hepatocarcinogens (GTHCs), 9 non-genotoxic hepatocarcinogens (NGTHCs), and 11 non-genotoxic non-hepatocarcinogens (NGTNHCs)]. As a result, 12 marker genes (Aen, Bax, Btg2, Ccnf, Ccng1, Cdkn1a, Gdf15, Lrp1, Mbd1, Phlda3, Plk2, and Tubb4b) were proposed to discriminate GTHCs from NGTHCs and NGTNHCs. U.S. Environmental Protection Agency studied DEGs induced by 4 known GTHCs in rat liver using DNA microarray and proposed 7 biomarker genes, Bax, Bcmp1, Btg2, Ccng1, Cdkn1a, Cgr19, and Mgmt for GTHCs. Studies involving the use of whole-transcriptome RNA-Seq upon exposure to chemical carcinogens in vivo have also been performed in rodent liver, kidney, lung, colon, and other organs, although discrimination of GTHCs from NGTHCs was not examined. Candidate genes published using RNA-Seq, qPCR, and DNA microarray will be useful for the future development of short-term in vivo studies of environmental carcinogens using RNA-Seq.

Chronic obstructive pulmonary disease (COPD) is incurable chronic disease which kills 3.3 million each year worldwide. Number of global cases of COPD is steadily rising alongside with life expectancy, disproportionally hitting middle-income countries like Russia and China, in such conditions, new approaches to the COPD management are desperately needed. DNA microarray technology is a powerful genomic tool that has the potential to uncover underlying COPD biological alteration and brings up revolutionized treatment option to clinicians. We executed systematic review studies of studies published in last 10 years regarding DNA microarray application in COPD management, with complacence to PRISMA criteria and using PubMed and Medline data bases as data source. Out of 920 identified papers, 39 were included in the final analysis. We concluded that Genome-wide expression profiling using DNA microarray technology has great potential in enhancing COPD management. Current studied proofed this method is reliable and possesses many potential applications such as individual at risk of COPD development recognition, early diagnosis of disease, COPD phenotype identification, exacerbation prediction, personalized treatment optioning and prospect of oncogenesis evaluation in patients with COPD. Despite all the proofed benefits of this technology, researchers are still in the early stage of exploring it's potential. Therefore, large clinical trials are still needed to set up standard for DNA microarray techniques usage implementation in COPD management guidelines, subsequently giving opportunity to clinicians for controlling or even eliminating COPD entirely.

Introduction: Chronic lymphocytic leukaemia (CLL) is the most frequent adult leukaemia in the Western world. The clinical presentation varies greatly, from very indolent cases to those with aggressive and fast advancing disease. This variation has significant implications for clinical approaches, therapeutic tactics, and, ultimately, survival durations from diagnosis. Acquired chromosomal aberrations play a key role in CLL aetiology. Due to difficulty to obtain abnormal metaphases for analysis, few methods such as fluorescence in-situ hybridization (FISH) and multiplex ligation-dependent probe assay (MLPA) were employed to detect chromosomal aberration however the methods are limited to specific locus only. Thus, this study is aimed to detect the chromosomal aberrations using DNA microarray platform. Methods: In this retrospective study, DNA archive obtained from 7 CLL patients which collected at diagnosis and subjected to Affymetrix CytoScan® 750K single nucleotide polymorphism (SNP) array following the manufacture procedure. The raw data obtained were analysed using the Chromosome Analysis Suite (ChAS) software (Affymetrix) using annotations of genome version GRCh38 (hg38). Result: Out of 7 patients, 4 of them showing deletion of 13q while 3 of them showing deletion of 14q in various region . Some of the deleted loci were too small (0.42-0.6Mb) to be detected by conventional cytogenetic analysis (CCA). There was also the presence of additional chromosomal aberrations that could be missed by CCA, FISH, or MLPA due to cryptic deletion or duplication that was as small as 0.4MB in size. Conclusion: The present study showed that low resolution chromosomal aberration was able to be detected using DNA microarray platform in comparison to CCA, FISH and MLPA. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is the most common primary liver cancer, with a rising worldwide burden due to a lack of efficient treatment techniques and diagnosis after it has metastasized. Therefore, small non‐coding RNA (miRNAs) as protein translation inhibitors are gaining attention that degrades or suppress specific gene transcripts, making it a prime strategy for oncogenes or tumor suppression. Systematic research with miRNAs in combination with Arsenic, which has been employed as a drug to treat several diseases, including cancer, was focused on cellular responses through interacting with multiple biological targets. The differential gene expression of the DNA microarray dataset (GSE48441) revealed the association of sterol, cholesterol, and lipid metabolic processes. With the aid of the network pharmacology approach, hsa‐mir‐335‐5p was uncovered to negatively regulate the important nodes driving the transport and utilization of essential compounds for the rapid growth and proliferation of cancer cells. The binding energies of the duplexes were validated by the minimal free energies of the mRNAs for hsa‐mir‐335‐5p, indicating energetically desirable binding association. The molecular interactions between hsa‐mir‐335‐5p, which interacts with the Argonaute protein in the RNA induced silencing complex, and the target‐specific genes were also investigated, revealing its susceptibility to be employed in in vitro studies. [ABSTRACT FROM AUTHOR]

• DNA polymerases catalyze primer extension on DNA microarrays to generate dsDNA libraries. • Psoralen-mediated photocrosslinking immobilizes the DNA on the surface. • Specific template degradation with T7 exonuclease yields ssDNA. • Enzymatic conversion is applicable to commercial DNA microarrays. • Base-modified dNTPs can be inserted during primer extension. DNA microarrays are very useful tools to study the realm of nucleic acids interactions at high throughput. The conventional approach to microarray synthesis employs phosphoramidite chemistry and yields unmodified DNA generally attached to a surface at the 3′ terminus. Having a freely accessible 3′–OH instead of 5′–OH is desirable too, and being able to introduce nucleoside analogs in a combinatorial manner is highly relevant in the context of nucleic acid therapeutics and in aptamer research. Here, we describe an enzymatic approach to the synthesis of high-density DNA microarrays that can also contain chemical modifications. The method uses a standard DNA microarray, to which a DNA primer is covalently bound through photocrosslinking. The extension of the primer with a DNA polymerase yields double-stranded DNA but is also amenable to the incorporation of modified dNTPs. Further processing with T7 exonuclease, which catalyzes the degradation of DNA in a specific (5′→3′) direction, results in template strand removal. Overall, the method produces surface-bound natural and non-natural DNA oligonucleotides, is applicable to commercial microarrays and paves the way for the preparation of combinatorial, chemically modified aptamer libraries. [ABSTRACT FROM AUTHOR]

Gene selection methods are critical in cancer classification, which depends on the expression of a small number of biomarker genes, which have been a significant issue of enormous recent studies. Microarray technology allows generating tumors gene expression datasets. Cancer classification based on these datasets commonly has a kind of small sample size against the number of genes involved and includes multiclass categories. In this paper, grey wolf algorithm was used for extracting notable features in the pre-processing stage, and deep neural network (DNN) was used as deep learning for improving the accuracy degree of cancer detection from three datasets, i.e., STAD (Stomach adenocarcinoma), LUAD (lung adenocarcinoma) and BRCA (breast invasive carcinoma). The proposed method achieved the highest accuracy for these three datasets. The proposed method was able to achieve accuracy close to 100. Furthermore, the proposed method was compared with linear support vector machine classification, RBF, the nearest neighbor, linear regression, one vs. all, Naive Bayes, and decision tree algorithms. The proposed method had 0.57 improvement on the LUAD dataset, 1.11 optimization on the STAD dataset, and 0.78 development on the BRCA dataset. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate the effects of Botryococcus terribilis ethanol extract (BTEE) on lipopolysaccharide (LPS)-induced inflammation in RAW264 cells. BTEE significantly attenuated LPS-induced nitric oxide production and inflammatory cytokines release, including Ccl2, Cox2, and Il6. On the other hand, several anti-inflammatory mediators, such as Pgc1β and Socs1, were increased in BTEE-treated cells. Further, we performed an untargeted whole-genome microarray analysis to explore the anti-inflammatory molecular mechanism of BTEE. Enrichment analysis showed BTEE significantly downregulated 'response to stimulus', 'locomotion', and 'immune system response' and upregulated 'cell cycle' gene ontologies in both 6- and 17-h post-LPS stimulation conditions. Pathway analysis revealed BTEE could downregulate the expressions of chemokines of the CC and CXC subfamily, and cytokines of the TNF family, TGFβ family, IL1-like, and class I helical. PPI analysis showed AXL receptor tyrosine kinase (Axl), a receptor tyrosine kinase from the TAM family, and its upstream transcription factors were downregulated in both conditions. Node neighborhood analysis showed several Axl coexpressed genes were also downregulated. Further, kinase enrichment and chemical perturbation analyses supported Axl inhibition in BTEE-treated conditions. Altogether, these findings suggest anti-inflammatory effects of BTEE that are mediated via the suppression of pro-inflammatory cytokines and predict its potential as an Axl inhibitor. [ABSTRACT FROM AUTHOR]

Sweat plays a critical role in human body, including thermoregulation and the maintenance of the skin environment and health. Hyperhidrosis and anhidrosis are caused by abnormalities in sweat secretion, resulting in severe skin conditions (pruritus and erythema). Bioactive peptide and pituitary adenylate cyclase-activating polypeptide (PACAP) was isolated and identified to activate adenylate cyclase in pituitary cells. Recently, it was reported that PACAP increases sweat secretion via PAC1R in mice and promotes the translocation of AQP5 to the cell membrane through increasing intracellular [Ca2+] via PAC1R in NCL-SG3 cells. However, intracellular signaling mechanisms by PACAP are poorly clarified. Here, we used PAC1R knockout (KO) mice and wild-type (WT) mice to observe changes in AQP5 localization and gene expression in sweat glands by PACAP treatment. Immunohistochemistry revealed that PACAP promoted the translocation of AQP5 to the lumen side in the eccrine gland via PAC1R. Furthermore, PACAP up-regulated the expression of genes (Ptgs2, Kcnn2, Cacna1s) involved in sweat secretion in WT mice. Moreover, PACAP treatment was found to down-regulate the Chrna1 gene expression in PAC1R KO mice. These genes were found to be involved in multiple pathways related to sweating. Our data provide a solid basis for future research initiatives in order to develop new therapies to treat sweating disorders. [ABSTRACT FROM AUTHOR]

Glutathione (GSH) has long been recognised for its antioxidant and detoxifying effects on the liver. The hepatoprotective effect of GSH involves the activation of antioxidative systems such as NRF2; however, details of the mechanisms remain limited. A comparative analysis of the biological events regulated by GSH under physiological and oxidative stress conditions has also not been reported. In this study, DNA microarray analysis was performed with four experiment arms including Control, GSH, hydrogen peroxide (HP), and GSH + HP treatment groups. The GSH-treated group exhibited a significant upregulation of genes clustered in cell proliferation, growth, and differentiation, particularly those related to MAPK, when compared with the Control group. Additionally, liver functions such as alcohol and cholesterol metabolic processes were significantly upregulated. On the other hand, in the HP-induced oxidative stress condition, GSH (GSH + HP group) demonstrated a significant activation of cell proliferation, cell cycle, and various signalling pathways (including TGFβ, MAPK, PI3K/AKT, and HIF-1) in comparison to the HP group. Furthermore, several disease-related pathways, such as chemical carcinogenesis–reactive oxygen species and fibrosis, were significantly downregulated in the GSH + HP group compared to the HP group. Collectively, our study provides a comprehensive analysis of the effects of GSH under both physiological and oxidative stress conditions. Our study provides essential insights to direct the utilisation of GSH as a supplement in the management of conditions associated with oxidative stress.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen that causes serious infections in healthcare facilities and in communities. The purpose of this study was to investigate MRSA isolates obtained in a tertiary hospital in Kuwait to assess their antibiotic susceptibility profile and clonal composition. Sixty MRSA isolates collected in 2020 were tested through antibiotic susceptibility testing, spa typing, and DNA microarray analysis. All isolates were found to be susceptible to vancomycin (MIC: ≤3 µg/mL), teicoplanin (MIC: ≤3 µg/mL), rifampicin, and mupirocin, but were resistant to fusidic acid (n = 43, 72%), trimethoprim (n = 27, 45%), ciprofloxacin (n = 31, 51.7%), gentamicin (n = 14; 23.3%), kanamycin (n = 20; 33.3%), chloramphenicol (n = 7; 11.7%), tetracycline (n = 17; 28.3%), erythromycin (n = 19; 31.6%), inducible clindamycin (n = 13; 21.7%), and constitutive clindamycin (n = 2; 3.3%). The isolates belonged to 30 spa types and 13 clonal complexes (CCs). The dominant spa types were t304, t442, t311, t688, and t1234, collectively constituting 28.3% of the isolates. The dominant CCs were CC5 and CC6, which together constituted 46.7% of the isolates. This study provides updated research on antibiotic resistance and changes in the clonal composition of MRSA in a Kuwait hospital, including the disappearance of the ST239-MRSA-III clone that was previously the dominant clone in this hospital.

Abstract A microarray detection method based on on-chip signal amplification using terminal deoxynucleotidyl transferase (TdT) was developed to visualize pathogenic genes. Cyclic olefin copolymer (COC) substrate for microarrays was treated with oxygen plasma to induce hydrophilic surface properties. The capture probe DNA was immobilized on the COC surface by UV irradiation. The 3ʹ end of the capture probe DNA immobilized on the COC surface was modified with a phosphate group to provide resistance against the TdT reaction. Therefore, the TdT reaction was triggered only when the capture probe DNA acquired the target gene, and biotin-11-deoxyuridine triphosphate (b-dUTP) was continuously added to the 3ʹ end of the target gene. Thereafter, streptavidin-conjugated gold nanoparticles (s-AuNPs) tagged the poly uridine tails by the biotin–streptavidin interaction. The visual signal was amplified by silver enhancement in the presence of the s-AuNPs. The usefulness of this detection method was confirmed by analyzing four pathogens and allowing their visual identification.

The performance in physical activity is determined not only by physiological processes such as age, body composition, gender and degree of training, but also by the genomics and even epigenetic events occurring during the training programs. In this context, using bioinformatics resources, we aimed to analyse the expression of genes associated with muscle function in vastus lateral samples. We used data from DNA microarray experiments reported in NCBI's GEO DataSet database under the series number GSE117070. Differential expression was calculated using the Z-ratio equation. We also used the software Cytoscape 3.6 to build a protein-protein interaction network with over-expressed genes. We found that seven genes out of the 397 genes analysed in the 41 individuals subjected to aerobic exercise with an increase in training intensity through the percentage of VO2max, were over-expressed based on the statistical approach. The Protein-Protein Interaction (PPI) network showed 477 nodes, two connected components, 17 multi-edge node pairs and an average number of neighbours of 2.092. The node with the highest number of interactions was TPM1 with 150. GO categories of biological processes most relevant of the network included indispensable processes for muscle function and contraction such as polymerization of actin filaments and ATP synthesis from electron transport chain.

Summary: With the rapid advancement of DNA microarray technologies, researchers in biology can now monitor several gene expression levels in one single experiment that is very useful in detecting or classifying specific types of tumors. The microarray data and its high‐dimensional nature, along with a small set of samples, have presented a new but well‐known phenomenon called the curse of dimensionality. The process of organizing all objects into various groups based on their traits that are either similar or dissimilar is known as clustering. The framework has the foundation of a minimum spanning tree (MST), which is the representation of one set of gene expression data that is multidimensional. The main property of such representations is that every cluster of this expression data will correspond to a subtree in the MST that can convert the problem of multidimensional Clustering to the problem of tree partitioning. A stochastic diffusion search (SDS) has been deployed for clustering. The algorithm was used to be a multi‐agent technique of search and optimization. A variable neighborhood search (VNS) algorithm has been proposed to be a metaheuristic that solves problems of global and combinatorial optimization. The goal of this method was proceeded to get a systematic change to the neighborhood in a local search algorithm. The algorithm will continue to remain the same as an optimal solution that explores the far neighborhoods until better solutions are identified. [ABSTRACT FROM AUTHOR]

The study aimed to understand mechanism/s of neuronal outgrowth in the rat adrenal-derived pheochromocytoma cell line (PC12) under pituitary adenylate cyclase-activating polypeptide (PACAP) treatment. Neurite projection elongation was suggested to be mediated via Pac1 receptor-mediated dephosphorylation of CRMP2, where GSK-3β, CDK5, and Rho/ROCK dephosphorylated CRMP2 within 3 h after addition of PACAP, but the dephosphorylation of CRMP2 by PACAP remained unclear. Thus, we attempted to identify the early factors in PACAP-induced neurite projection elongation via omics-based transcriptomic (whole genome DNA microarray) and proteomic (TMT-labeled liquid chromatography-tandem mass spectrometry) analyses of gene and protein expression profiles from 5–120 min after PACAP addition. The results revealed a number of key regulators involved in neurite outgrowth, including known ones, called 'Initial Early Factors', e.g., genes Inhba, Fst, Nr4a1,2,3, FAT4, Axin2, and proteins Mis12, Cdk13, Bcl91, CDC42, including categories of 'serotonergic synapse, neuropeptide and neurogenesis, and axon guidance'. cAMP signaling and PI3K-Akt signaling pathways and a calcium signaling pathway might be involved in CRMP2 dephosphorylation. Cross-referencing previous research, we tried to map these molecular components onto potential pathways, and we may provide important new information on molecular mechanisms of neuronal differentiation induced by PACAP. Gene and protein expression data are publicly available at NCBI GSE223333 and ProteomeXchange, identifier PXD039992. [ABSTRACT FROM AUTHOR]

Next-generation RNA sequencing (RNA-Seq) has identified more differentially expressed protein-coding genes (DEGs) and provided a wider quantitative range of expression level changes than conventional DNA microarrays. JEMS·MMS·Toxicogenomics group studied DEGs with targeted RNA-Seq on freshly frozen rat liver tissues and on formalin-fixed paraffin-embedded (FFPE) rat liver tissues after 28 days of treatment with chemicals and quantitative real-time PCR (qPCR) on rat and mouse liver tissues after 4 to 48 h treatment with chemicals and analyzed by principal component analysis (PCA) as statics. Analysis of rat public DNA microarray data (Open TG-GATEs) was also performed. In total, 35 chemicals were analyzed [15 genotoxic hepatocarcinogens (GTHCs), 9 non-genotoxic hepatocarcinogens (NGTHCs), and 11 non-genotoxic non-hepatocarcinogens (NGTNHCs)]. As a result, 12 marker genes (Aen, Bax, Btg2, Ccnf, Ccng1, Cdkn1a, Gdf15, Lrp1, Mbd1, Phlda3, Plk2, and Tubb4b) were proposed to discriminate GTHCs from NGTHCs and NGTNHCs. U.S. Environmental Protection Agency studied DEGs induced by 4 known GTHCs in rat liver using DNA microarray and proposed 7 biomarker genes, Bax, Bcmp1, Btg2, Ccng1, Cdkn1a, Cgr19, and Mgmt for GTHCs. Studies involving the use of whole-transcriptome RNA-Seq upon exposure to chemical carcinogens in vivo have also been performed in rodent liver, kidney, lung, colon, and other organs, although discrimination of GTHCs from NGTHCs was not examined. Candidate genes published using RNA-Seq, qPCR, and DNA microarray will be useful for the future development of short-term in vivo studies of environmental carcinogens using RNA-Seq. [ABSTRACT FROM AUTHOR]