Characterization of the early fiber development gene, Ligon-lintless 1 (Li1), using microarray

AbstractCotton fiber length is a key factor in determining fiber quality in the textile industry throughout the world. Understanding the molecular basis of fiber elongation would allow for improvement of fiber length. Ligon-lintless 1 (Li1) is a monogenic dominant mutation that results in short fibers. This mutant provides an excellent model system to study the molecular mechanisms of cotton fiber elongation. Microarray technology and quantitative real time PCR (qRT-PCR) were used to evaluate differentially expressed genes (DEGs) in the Ligon-lintless 1 (Li1) mutant compared to the wild-type. Although the results showed only a few differentially expressed genes at −1, 3 and 7days post anthesis (DPA); at 5 DPA, there were 1915 DEGs, including 984 up-regulated genes and 931 down-regulated genes. The critical stage for early termination of Li1 fiber elongation was 5 DPA, as there were the most differentially expressed genes in this sample. The transcription factors and other proteins identified might contribute to understanding the molecular basis of early fiber elongation. Gene ontology analysis identified some key GO terms that impact the regulation of fiber development during early elongation. These results provide some fundamental information about the TFs that might provide new insight into understanding the molecular mechanisms governing cotton fiber development

Detection of Bcl-2 gene in leukaemic rats using an EvaGreen real-time RT-PCT assay

Bcl-2 is an anti-apoptotic gene that is involved in the apoptosis process. Suppression of apoptosis by anti- apoptotic gene can contribute to the occurrence of diseases such as leukaemia. The objectives of this study were 2-folds: first, to compare the sensitivity of an EvaGreen quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) with a conventional RT-PCR for the amplification of the Bcl-2 gene; second, to determine the expression of the Bcl-2 gene in N-methyl-N-nitrosourea (MNU)-induced leukaemiain rats using the EvaGreen qRT-PCR assay. A total of 32 male Sprague Dawley rats were assigned into two groups (n=16), namely, control and MNU groups. In particular, MNU was administered intraperitoneally (i.p) at a dose of 60 mg/kg body weight per injection at two times per week for 2 consecutive weeks. The rats were sacrificed after five months and blood samples were collected for RNA extraction and haemogram. The RNAs were converted into cDNA and amplified using both the EvaGreen qPCR and the conventional PCR assays. All the results were normalised with a housekeeper gene, i.e. glyceraldehyde 3-phosphate dehydrogenase (GADPH). The products of amplification were run on gel electrophoresis and all the results were then compared. Based on the relative intensity of the bands, the EvaGreen qRT-PCR assay was highly sensitive compared to the conventional RT-PCR assay as the Bcl-2 gene could not be amplified using the conventional RT-PCR. Interestingly, the results in this study showed that the expression of Bcl-2 was higher in rats with marked lymphocytosis as compared to the leukaemic rats with normal to mildly increase in lymphocyte count. In conclusion, EvaGreen qRT-PCR assay is more sensitive compared to the conventional RT-PCR, and Bcl-2 gene is abundantly expressed in leukaemic rats with marked lymphocytosis compared to the leukaemic rats with normal to mildly increase in lymphocyte number

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Genome-wide characterization, identification and expression analysis of WD40 proteins family in cotton

Abstract WD40 repeat proteins are largely distributed across the plant kingdom and played an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization and expression level analysis of WD40 genes in cotton. A total of 579, 318 and 313 WD40 genes were found in Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950 and miR7505. The findings provide a stronger indication of WD40 gene functions and their involvement in the regulation of cotton fiber development during initiation and elongation stages.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species

Genome-Wide Identification and Comparative Analysis of MYB Transcription Factor Family in Musa acuminata and Musa balbisiana

MYB transcription factors (TFs) make up one of the most important TF families in plants. These proteins play crucial roles in processes related to development, metabolism, and stimulus-response; however, very few studies have been reported for the characterization of MYB TFs from banana. The current study identified 305 and 251 MYB genes from Musa acuminata and Musa balbisiana, respectively. Comprehensive details of MYBs are reported in terms of gene structure, protein domain, chromosomal localization, phylogeny, and expression patterns. Based on the exon–intron arrangement, these genes were classified into 12 gene models. Phylogenetic analysis of MYBs involving both species of banana, Oryza sativa, and Arabidopsis thaliana distributed these genes into 27 subfamilies. This highlighted not only the conservation, but also the gain/loss of MYBs in banana. Such genes are important candidates for future functional investigations. The MYB genes in both species exhibited a random distribution on chromosomes with variable densities. Estimation of gene duplication events revealed that segmental duplications represented the major factor behind MYB gene family expansion in banana. Expression profiles of MYB genes were also explored for their potential involvement in acetylene response or development. Collectively, the current comprehensive analysis of MYB genes in both species of banana will facilitate future functional studies

Systematic Review of Computing Approaches for Breast Cancer Detection Based Computer Aided Diagnosis Using Mammogram Images

Breast cancer is one of the most prevalent types of cancer that plagues females. Mortality from breast cancer could be reduced by diagnosing and identifying it at an early stage. To detect breast cancer, various imaging modalities can be used, such as mammography. Computer-Aided Detection/Diagnosis (CAD) systems can assist an expert radiologist to diagnose breast cancer at an early stage. This paper introduces the findings of a systematic review that seeks to examine the state-of-the-art CAD systems for breast cancer detection. This review is based on 118 publications published in 2018–2021 and retrieved from major scientific publication databases while using a rigorous methodology of a systematic review. We provide a general description and analysis of existing CAD systems that use machine learning methods as well as their current state based on mammogram image modalities and classification methods. This systematic review presents all stages of CAD including pre-processing, segmentation, feature extraction, feature selection, and classification. We identify research gaps and outline recommendations for future research. This systematic review may be helpful for both clinicians, who use CAD systems for early diagnosis of breast cancer, as well as for researchers to find knowledge gaps and create more contributions for breast cancer diagnostics

Additional file 4: Table S3. of Genome-wide characterization and expression analysis of MYB transcription factors in Gossypium hirsutum

Location of MYB genes in the upland cotton genome. The positive (+) and negative (−) symbols following each gene represent forward and reverse orientations on the chromosome, respectively. (XLSX 45 kb