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Volcano plot for comparison between COVID-19 infected individuals and healthy. The X-axis shows log₂ fold change (positive values are up regulated relative to healthy. The Yaxis shows the −log10 of BH adjusted p-value (padj) value. The horizontal dashed line marks P= 1%, and the vertical dashed lines indicate two-fold expression difference among conditions. The differentially expressed genes are indicated in red according to a P<.01, green points represent genes not passing the threshold, and grey points represent genes with no significant difference.
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The clinical presentation overlap between malaria and COVID-19 poses special challenges for rapid diagnosis in febrile children. In this study, we collected RNA-seq data of children with malaria and COVID-19 infection from the public databases as raw data in fastq format paired end files. A group of six, five and two biological replicates of malari...
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... and we considered a fold change adjusted p-value (padj) value < 0.1 as significant. The volcano plot highlights differences in gene expression with the key genes involved in the host responses. There we observed an upregulation of key genes involved in the host responses, such as SLC12A5-AS1, RAP1GAP, TCF3, STB1, CCDC124, IFI27, and CD177 (Fig. 4). ...
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... total of 3,579 genes were differentially expressed in our RNA seq datasets. The comparison of COVID-19 samples relative to healthy samples we found that about 2495 genes differentially expressed such as SLC12A5-AS1, ENSG00000234998, GPS2P1, RCCD1-AS1 and RAP1GAP (Fig. 4). The high expression of SLC12A5-AS1 is a lncRNA gene associated with NK-cell in the lung and can respond to viral infections [37]. We also found the upregulation of ENSG00000234998 as a novel transcript belonging to the class of lncRNA, associated with CD64, which is the receptors of SARS-CoV-2 [38]. These receptors have been reported ...
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... and we considered a fold change adjusted p-value (padj) value < 0.1 as significant. The volcano plot highlights differences in gene expression with the key genes involved in the host responses. There we observed an upregulation of key genes involved in the host responses, such as SLC12A5-AS1, RAP1GAP, TCF3, STB1, CCDC124, IFI27, and CD177 (Fig. 4). ...
Context 4
... total of 3,579 genes were differentially expressed in our RNA seq datasets. The comparison of COVID-19 samples relative to healthy samples we found that about 2495 genes differentially expressed such as SLC12A5-AS1, ENSG00000234998, GPS2P1, RCCD1-AS1 and RAP1GAP (Fig. 4). The high expression of SLC12A5-AS1 is a lncRNA gene associated with NK-cell in the lung and can respond to viral infections [37]. We also found the upregulation of ENSG00000234998 as a novel transcript belonging to the class of lncRNA, associated with CD64, which is the receptors of SARS-CoV-2 [38]. These receptors have been reported ...
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Background
Over the past few decades, the emergence and maturation of new technologies have substantially reduced the cost of genome sequencing. As a result, the amount of genomic data that needs to be stored and transmitted has grown exponentially. For the standard sequencing data format, FASTQ, compression of the quality score is a key and diffic...
Citations
... Furthermore, PIT1 co-localized with TXNDC5 is required for ER homeostasis, chondrocyte survival, and skeletal development [197], also TXNDC5 knockdown is highly toxic to osteosarcoma cells, possibly implying that it has a critical function in cells that endogenously express collagen-I [198]. Other studies have identified an upregulation of TXNDC5 in Parkinson's disease, respiratory distress syndrome following cardiopulmonary bypass, COVID-19, malaria, Salmonella enteritidis and Marek's disease infection [199][200][201][202][203][204]. However, TNFRSF17 and TXNDC5 are the target genes for the COVID-19 vaccine [205]. ...
This review focuses on the thioredoxin domain containing 5 (TXNDC5), also known as endoplasmic reticulum protein 46 (ERp46), a member of the protein disulfide isomerase (PDI) family with a dual role in multiple diseases. TXNDC5 is highly expressed in endothelial cells, fibroblasts, pancreatic β-cells, liver cells, and hypoxic tissues, such as cancer endothelial cells and atherosclerotic plaques. TXNDC5 plays a crucial role in regulating cell proliferation, apoptosis, migration, and antioxidative stress. Its potential significance in cancer warrants further investigation, given the altered and highly adaptable metabolism of tumor cells. It has been reported that both high and low levels of TXNDC5 expression are associated with multiple diseases, such as arthritis, cancer, diabetes, brain diseases, and infections, as well as worse prognoses. TXNDC5 has been attributed to both oncogenic and tumor-suppressive features. It has been concluded that in cancer, TXNDC5 acts as a foe and responds to metabolic and cellular stress signals to promote the survival of tumor cells against apoptosis. Conversely, in normal cells, TXNDC5 acts as a friend to safeguard cells against oxidative and endoplasmic reticulum stress. Therefore, TXNDC5 could serve as a viable biomarker or even a potential pharmacological target.
... Its over expression has been linked to unrestricted cell proliferation, tumor development, and dysregulation associated with the initiation of many cancers including colorectal cancer (Li et al., 2020;Sofi et al., 2022a;Sofi et al., 2022b). Gene expression has been associated with biomarkers in complex diseases like prostate cancer (Chikwambi et al., 2023), epilepsy (El Abed et al., 2023), malaria/COVID-19 (Nzungize et al., 2022) and SARS-CoV-2 infection . Several studies suggest that overexpression of CDK1, which is the hallmark event in many malignancies is associated with 5 = fluorouracil resistance through altered activation of Wnt/β-catechin signaling, mTOR, and p53 pathways leading to poor prognosis in CRC (Zhu et al., 2019;Zhu et al., 2020a;Zhu et al., 2020b;Sofi et al., 2022a). ...
Introduction: Despite improved treatment options, colorectal cancer (CRC) remains a huge public health concern with a significant impact on affected individuals. Cell cycle dysregulation and overexpression of certain regulators and checkpoint activators are important recurring events in the progression of cancer. Cyclin-dependent kinase 1 (CDK1), a key regulator of the cell cycle component central to the uncontrolled proliferation of malignant cells, has been reportedly implicated in CRC. This study aimed to identify CDK1 inhibitors with potential for clinical drug research in CRC.
Methods: Ten thousand (10,000) naturally occurring compounds were evaluated for their inhibitory efficacies against CDK1 through molecular docking studies. The stability of the lead compounds in complex with CDK1 was evaluated using molecular dynamics simulation for one thousand (1,000) nanoseconds. The top-scoring candidates’ ADME characteristics and drug-likeness were profiled using SwissADME.
Results: Four hit compounds, namely, spiraeoside, robinetin, 6-hydroxyluteolin, and quercetagetin were identified from molecular docking analysis to possess the least binding scores. Molecular dynamics simulation revealed that robinetin and 6-hydroxyluteolin complexes were stable within the binding pocket of the CDK1 protein.
Discussion: The findings from this study provide insight into novel candidates with specific inhibitory CDK1 activities that can be further investigated through animal testing, clinical trials, and drug development research for CRC treatment.
... Among these 14 genes (Table S2), some of them are reported to be closely related to COVID-19. RNF187 has been shown to be a biomarker in children with COVID-19 [22]; NCR3 is significantly associated with the decreased proportion of CD8+ T and T helper 2 cells in the peripheral circulation in COVID-19 patients [23]; TEX2 can predict the ventilator-free days of patients with COVID-19 [24]; ITPKB is a hub gene shared by Alzheimer's disease and COVID-19 [25]; TUBG1 is involved in the immune interaction of COVID-19 and lymphoma [26]; RPL14 is a significantly upregulated gene in COVID-19 patients [27]. Besides the above genes, other unreported genes in the AGAE score may also have research significance. ...
Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
