Search

Introduction. Taxonomy is an effective mean of managing and accessing a large amount of digital information. Various techniques have been developed to generate taxonomy automatically. The purpose of this study is threefold: (i) review methods and approaches adopted during taxonomy generation, (ii) identify the factors influencing the choice of a particular method or approach, (iii) highlight issues and open challenges. Method. This paper adopts a systematic literature review approach proposed by Kitchenham, and the nature of this review is qualitative. Analysis. A total of thirty techniques were reviewed and categorized into various categories and subcategories. An in-depth analysis of the existing techniques was performed based on this categorization. This ultimately helps in identifying factors influencing the choice of a particular method or approach, and also determines issues and challenges associated with the automatic taxonomy generation. Results. Four major factors influencing the choice of a particular method or approach for generating taxonomy have been identified. Moreover, five major challenges associated with the existing automatic taxonomy generation techniques have also been highlighted. Conclusions. This paper presents a comprehensive review of taxonomy generation so that taxonomy can be used effectively, and it highlights open challenges for future research in the area of taxonomy generation so that new and improved techniques can be developed.

Introduction: Carbapenem-resistant Enterobacterales (CRE), particularly carbapenemase-producing Escherichia coli and Klebsiella pneumoniae , pose a significant global health challenge due to their resistance to last-resort antibiotics. This study investigates the genetic characteristics and clonal relationships of CRE isolated from canine and human clinical samples in Bangkok to understand potential interspecies transmission. Methods: Fifty-two CRE isolates were collected from 477 clinical samples from dogs and humans at Chulalongkorn University between 2017–2021. Bacterial species were identified using MALDI-TOF, and antimicrobial resistance was confirmed through broth microdilution testing. Genetic analyses included plasmid replicon typing, multilocus sequence typing (MLST), whole genome sequencing (WGS), and pulsed-field gel electrophoresis (PFGE) to assess resistance genes and clonal relatedness. Results: CRE isolates from both species exhibited genetic variability with high ARG counts, particularly in human isolates. MLST identified ST410 in most E. coli isolates from both dogs and humans, and IncFIA/IncFIB plasmids were predominant among blaNDM-positive isolates. PFGE patterns and SNP analysis showed no clonal relationship between canine and human isolates, suggesting independent acquisition pathways for CRE in the two hosts. Discussion: The study highlights the absence of direct clonal transmission between canine and human isolates but reveals overlapping sequence types and plasmid types. The findings underscore the potential for interspecies transmission under certain conditions, emphasizing the importance of a One Health approach for monitoring CRE in both human and animal populations. [ABSTRACT FROM AUTHOR]

Heat stress represents a significant environmental challenge that restricts maize (Zea mays) growth and yield on a global scale. Within the plant kingdom, the AGC gene family, encoding a group of protein kinases, has emerged as crucial players in various stress responses. Nevertheless, a comprehensive understanding of AGC genes in Z. mays under heat-stress conditions remains elusive. A genome-wide analysis was done using bioinformatics techniques to identify 39 AGC genes in Z. mays , categorising them into three subfamilies based on their conserved domains. We investigated their phylogenetic relationships, gene structures (including intron-exon configurations), and expression patterns. These genes are likely involved in diverse signalling pathways, fulfilling distinct roles when exposed to heat stress conditions. Notably, most ZmAGC1.5, ZmAGC1.9, ZmNDR3, ZmNDR5 and ZmIRE3 exhibited significant changes in expression levels under heat stress, featuring a high G-box ratio. Furthermore, we pinpointed a subset of AGC genes displaying highly coordinated expression, implying their potential involvement in the heat stress response pathway. Our study offers valuable insights into the contribution of AGC genes to Z. mays 's heat stress response, thus facilitating the development of heat-tolerant Z. mays varieties. Rising global temperature is negatively affecting maize yield. Current genome-wide analysis identified and characterised AGC genes, one of the major contributors of plant stress response. Heat stress mediated differential expression of AGCs (using RNA-seq and real time qPCR) underscore the potential for developing heat-tolerant maize varieties by understanding the intricate workings of these genes. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

Helicobacter pylori causes gastritis, ulcer and gastric cancer. Bacterial infections may lead to epigenetics alteration via Sirtuin 2 in inflammatory and carcinogenesis process. In this case control study, expression of Sirt2 gene in gastric cancer with respect to H. pylori was investigated. A total of 20 biopsies samples were obtained from patients with GI disturbances and gastric cancer. H. pylori was detected in staining, biochemical and species-specific PCR. After confirmation of H. pylori, total RNA was extracted for cDNA synthesis from gastric cancer biopsy of case and control samples. Real Time PCR was used to check the expression of Sirt2 gene. Among the 20 biopsies, gastric ulcer (n=5), gastritis (n=2) and gastric cancer (n=12) were diagnosed with endoscopy and histopathology. H. pylori was confirmed in three samples of gastric cancer. On real time PCR, the expression of Sirt2 gene was increased by 2.6-fold; however non-significant (p> 0.05) correlation was observed between case and control samples. Findings of this study will help in H. pylori role in gastric cancer via Sirt2 gene expression. [ABSTRACT FROM AUTHOR]

Carbapenem-resistant Acinetobacter baumannii (CRAB) produce resistance to various classes of antibiotics and left limited options for treatment. This study was designed to determine antibacterial activity of AgNPs against CRAB. Total 100 A. baumannii were collected from a tertiary care hospital, Lahore. Isolates were subcultured on blood and MacConkey agar. Preliminary identification was carried out by morphological and biochemical tests. Antibiogram was done by Kirby-Bauer disc diffusion method. Antibacterial activity of AgNPs was performed by agar well diffusion method, while minimum inhibitory concentration and minimum bactericidal concentration were determined by micro broth dilution assay. Of 100 A. baumannii, 24 were confirmed as carbapenem-resistant. These isolates were mainly recovered from tracheal secretion (8; 33%), CSF (5; 20.8%), and urine (4; 16.8%). Antibacterial activity of AgNPs revealed a maximum zone of inhibition, 22mm at 50mg/mL and 18mm at 40mg/mL by agar well diffusion method. MIC of AgNPs determined that 14 CRAB were inhibited at 12.5mg/mL and 7 at 25mg/mL. However, MBC revealed that 13 CRAB were killed at 25mg/mL and 7 at 50mg/mL. This study concluded that most of the CRAB were inhibited and killed at 12.5mg/mL and 25mg/mL, respectively. AgNPs can be used as an alternative therapeutic agent followed by their pharmacokinetics and pharmacognosy. [ABSTRACT FROM AUTHOR]