Baobab Index

Escherichia coli (E. coli) F17 is one of the leading bacterial causes of diarrhea in farm livestock, which cause huge economic losses and could also pose potential risks to public health. Generally, the monitoring the E. coli F17 is based on the polymerase chain reaction (PCR) and bacteria plate counting method, which were largely limited by the time-consuming nature and susceptibility to detection errors. Hence, there is an urgent need to develop a rapid and quantitative detection method for E. coli F17. In the present study, an E. coli F17 challenge experiment in ovine intestinal epithelial cells (IECs) was employed as an in vitro model. At different post-challenge time points (1 h, 2 h, and 3 h), two conventional methods (bacteria plate counting and microplate method) were conducted as benchmarks to estimate the number of E. coli F17 adhering to the IECs. Additionally, total genomic DNA was extracted and quantitative Real-time PCR (qPCR) was performed to detect the relative abundance of E. coli F17 fimbrial pilin (F17-A) and adhesion (F17-G) genes. Subsequently, statistical analyses, including Pearson's correlation coefficient (PCC) method and linear curve-fitting, were performed to evaluate the correlation between the abundance of F17-A/G genes and the results of the benchmark methods. The results showed that the relative abundances of both genes were highly correlated with the number of E. coli F17 that adhered to the IECs, among them, the F17-A gene showed a stronger correlation with the bacterial counts, exhibiting a correlation coefficient > 0.85. Furthermore, standard curves analyses further confirmed the out-performed quantitative performance of F17-A gene and a significantly stronger correlation with bacterial counts which exhibited an outstanding linear correlation (r = -0.9534, R

Medicinal and aromatic plants (MAPs) produce a remarkable diversity of specialized metabolites with significant pharmaceutical, nutraceutical, and industrial value. Although advances in long-read sequencing, chromosome-scale genome assembly, and pangenomics have greatly expanded genomic resources, the mechanistic links between genome architecture and phytochemical diversity remain incompletely understood. The present review synthesizes current evidence describing how structural genomic variation may contribute to phytochemical diversity, while acknowledging that many proposed genome-to-metabolite relationships require further experimental validation. Examples illustrate how genome architecture is associated with specialized-metabolite biosynthesis through multiple regulatory processes. However, the strength of supporting evidence varies considerably among MAP species. Moreover, relatively few genome-to-metabolite relationships have been confirmed through direct functional validation. We further discuss how pangenomics, multiomics integration, genome editing, synthetic biology, and artificial intelligence support the discovery, validation, and engineering of specialized metabolic pathways. Casual conclusions are evaluated according to the strength of available evidence, highlighting where causal relationships have been experimentally established and where conclusions remain primarily association-based. Overall, this review provides an integrated conceptual and evidence-based perspective summarizing proposed relationships between genome architecture and phytochemical diversity and outlines future priorities for functional genomics, precision breeding, metabolic engineering, and sustainable utilization of MAPs.

A study was conducted to characterize four autochthonous chicken ecotypes of Ethiopia using selected phenotypic traits. Data were collected from a total of 191 chickens, including reproductive traits such as age at first egg, first egg weight, egg number at 250 days, egg weight at 250 days, hatchability and fertility. Morphometric measurements were recorded at 24 weeks of age from 40 cocks and 151 hens, including body weight and linear body dimensions. Both univariate and multivariate statistical analyses were performed using SAS software. The results revealed moderate variation among ecotypes, with significant differences observed in age at first egg, first egg weight, and egg number at 250 days. Principal Component Analysis (PCA) was used to identify key traits contributing to variation. In female chickens, the first two principal components (PC1 and PC2) explained 76.13% of the total variation, while in males, the first three principal components (PC1, PC2, and PC3) accounted for 72.14% of the total variation. Key discriminating traits in males included shank length, shank circumference, neck length, wattle width, and wing span, whereas in females, shank length, beak length, wattle length, keel length, and wing span were the most important distinguishing features. In conclusion, the observed phenotypic variability indicates the potential for selection and genetic improvement of indigenous chicken ecotypes. However, integrating molecular characterization is recommended to validate morphological differences and enhance breeding programs.

Wood processing industries generate staggering volumes of sawdust and residues. This research created a new way to turn wood waste into valuable resources, solving both environmental problems and agricultural challenges. Through step-by-step valorization pathways, sawdust was reused as a soil enhancer and processed into functional cellulose particles using chemical treatments-alkali digestion, peroxide bleaching, and acid hydrolysis. Characterization tests included: Zeta potential and size, Scanning electron microscope (SEM) and FT-IR. The zeta size showed nanocellulose populations at 95.82 nm and submicron cellulose (412.0 nm), with FT-IR spectroscopy proved they kept their natural structure by showing distinct hydroxyl (3339 cm⁻¹), hydrocarbon (2926 cm⁻¹), and glycosidic bond (1031 cm⁻¹) signatures. Scanning electron microscopy visualized the morphological transition from raw wood shavings to nano/micro-scale cellulose fibrils. This study used wood waste in four applications: water conservation, agriculture enhancement, bioremediation and medical wound healing. Sawdust reveals high water conservation within its particles due to high porosity on its surface. In agronomic trials with barley plant, the soil mixed with cellulose particles (S + C) significantly enhanced root development (11.5 cm) while keeping robust shoot elongation (23.5 cm), though sawdust-enriched soil (S + W) unexpectedly contained the highest leaf protein concentration (149.14 µg/mL). Genetic analysis confirmed all treatments induced low DNA variants, proving genomic safety. The polymorphism percentage from RAPD-PCR was 22.5%, while the polymorphism of SCoT-PCR was 13.7%. The extracted cellulose particles worked well in environmental remediation, reducing synthetic dye concentrations, and accelerated wound healing in cellular models. This work serves to achieve about seven goals of Sustainable Development Goals (SDGs) related to food, health, environment and climatic changes: SDG 2, 3, 6, 9, 12, 13 and 15.

CRISPR/Cas9 has emerged as a powerful tool for editing of non-coding sequence, such as promoters and enhancers. Creating indels in enhancer sequences alter their function and provide valuable insights into their role in gene expression under normal and pathological conditions. This study tested the involvement of CD44-upstream cis-element in regulating CD44 expression and evaluated the potential of CRISPR/Cas9 system to manipulate the transcription factor (TF) binding site within this element. Bioinformatic tools predicted two binding sites (designated P1 and P2) for NFYA within the cis-element sequence. CRISPR/Cas9-mediated genome editing was employed to knockout NFYA gene and disrupt the NFYA-binding site at P2 in MDA-MB-231 breast cancer cells, then downstream analysis was performed using the mixed-edited cell population. Both genome editing strategies resulted in a significant reduction in CD44 gene expression at mRNA level. Notably, disruption of P2 sequence produced a greater reduction in the CD44

Generalized Arterial Calcification of Infancy (GACI) is a rare genetic vascular disease characterized by the early onset (between in utero and infancy) of extensive calcification and stenosis of the large and medium-sized arteries. Presentation is typically with respiratory distress, congestive heart failure, and systemic hypertension. With approximately 300 cases reported worldwide in the medical literature. The prevalence is unknown; however, based on the carrier frequency of the recognized pathogenic variants, a frequency of 1 in 200,000 has been suggested. The autosomal recessive form of GACI disorder is caused by mutations in the ENPP1 or ABCC6 genes. To the best of our knowledge, this study represents the first genetically confirmed case of GACI in an Egyptian fetus detected during the perinatal period. In this report, we describe a case of GACI in a fetus with a pathogenic ENPP1 gene mutation at 29 weeks of gestation. Ultrasound examination revealed aortic and pulmonary valve stenosis, biventricular hypertrophy, and a hypercalcified aorta and ductal arch. Genetic testing identified a homozygous pathogenic variant in the ENPP1 gene: c.749C>T (p.Pro250Leu). In conclusion, early diagnosis of GACI is vital due to its severe prognosis and early symptom onset. Expert fetal echocardiography plays a key role in detecting arterial calcification during pregnancy. Genetic testing enhances diagnostic accuracy, informs treatment strategies, and supports family counselling.

Conotruncal heart defects (CTDs) account for approximately one-third of all congenital heart defects. Elevated levels of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) may contribute to CTD pathogenesis. PIP3 plays a pivotal role in mechanotransduction-based biological processes and remodeling of cardiac cytoskeletal proteins. Here, we aimed to evaluate the efficacy of the 322PESB derivative compound as a molecular regulator that antagonizes PIP3 binding pleckstrin homology (PH) domain of the Akt protein using mesenchymal stem cell-derived cardiomyocyte. Human adipose-derived MSCs (Ad-MSCs) were isolated. Immunophenotypic features of the hAd-MSCs were characterized according to minimal criteria of the international society for cellular therapy (ISCT) including immunophenotyping and trilineage differentiation potential. Subsequently, the differentiated hAd-MSCs were cultured in cardiomyogenesis-inducing medium. Successfully differentiated cardiomyocytes were assessed by measuring the expression levels of cardiomyocyte-specific genes using RT-qPCR. PIP3-primed cardiomyocytes were treated with 10 and 30 μmol/L of a 322PESB derivative molecule. The results showed a typical MSCs with high expression levels of CD73 (77.55%), CD90 (87.59%) and CD105 (91.88%) and that was accompanied by low expression levels of CD34 (0.59%) and CD45 (1.78%). After 21 days of MSC culture, cardiomyocyte-like cells with prominent striations were observed. Subsequent confirmation by RT-qPCR quantification of ADRB1 and MLC2a expression levels showed an average increase of 2.9-fold and 2.1-fold, respectively, in induced cardiomyocytes. Compared with the untreated control, PIP3 ELISA assay showed a significant increase in PIP3 levels in PIP3(10 nmol/L)-primed cardiomyocytes treated with 10 and 30 μmol/L of the 322PESB molecule derivative by 485.804 and 3564.164 ng/mL, respectively. In this study, we conducted the first promising molecular regulator with potential therapeutic implications for CTD patients. Further functional animal model and clinical phase studies are recommended.

Advances in next-generation sequencing have accelerated genome-wide exploration of genetic diversity in underutilized oilseed crops. Salvia hispanica L. (chia), a high-nutrient pseudocereal rich in omega-3 fatty acids, is increasingly valued for its health benefits and commercial potential, yet it remains poorly characterized at the genomic level. Understanding the scale and nature of genomic variation is essential for improving complex traits such as oil yield, stress tolerance, and seed quality. Two contrasting chia genotypes, Black-chia (CACH-B) and White- chia (CACH-W), were resequenced using the Bio-Resequencing Toolkit (BRT) pipeline. High-coverage sequencing, with a mapping rate exceeding 99% and an average depth of approximately 28×, facilitated the detection and annotation of single-nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy-number variations (CNVs), and structural variants (SVs). The functional classification of variant impacts enabled the identification of genes potentially linked to metabolic and adaptive traits. A total of 1.97 million SNPs, 401,493 InDels, 836 CNVs, and 15,288 SVs were identified across the chia genome. Notably, approximately 53% of exonic SNPs were non-synonymous (dN/dS ≈ 1.28), predominantly affecting lipid metabolism, transcriptional regulation, and stress response pathways, potentially altering key agronomic traits. In addition, CNV hotspots were concentrated in chromosomes 3 and 6, overlapping MYB, WRKY, and bZIP transcription factor loci, may potentially be involved in stress tolerance and yield. Furthermore, structural rearrangements, including inversions and duplications within the FAD2, FAD3, and CYP450 gene clusters, were potentially associated with seed pigmentation and omega-3 biosynthesis, pointing to their potential breeding relevance. Observed heterozygosity (Hₒ ≈ 0.71) and nucleotide diversity (π ≈ 7 × 10 This study presents the first comprehensive map integrating SNPs, CNVs, and SVs in S. hispanica L. The results reveal a structurally dynamic genome characterized by substantial sequence and structural variation, providing valuable insights into genomic diversity and potential adaptive mechanisms in chia. The coexistence of high SNP diversity and abundant structural variation underpins chia's nutritional specialization and environmental resilience. These results deliver a foundational genomic resource for marker-assisted breeding, genome-wide association studies, and the development of climate-resilient chia cultivars.