Baobab Index

Metagenomic binning is a pivotal step in reconstructing metagenome-assembled genomes (MAGs) from complex microbial communities, and it critically depends on reliable measures of similarity between contigs. In many workflows, tetranucleotide-frequency (TNF) distances are translated into probabilistic evidence of a shared genome of origin. Despite their central role, these distances are often modeled with convenient but poorly matched assumptions, even though they are intrinsically non-negative and frequently exhibit pronounced right-skewness-features that can distort tail behavior and weaken downstream thresholding decisions. In this work, we introduce a likelihood-based framework for characterizing intra- and inter-genomic TNF distance distributions with flexible right-skewed parametric models and for converting fitted distributions into calibrated distance-to-probability scores within a MaxBin-style scheme. Our approach provides a principled statistical basis for distributional assessment, probability calibration, and transparent operating-point selection, with the goal of improving robustness and interpretability in TNF-driven binning. All codes related to the article are available through a public GitHub repository at https://github.com/omar-hajjaji/Calibrating-TNF-Distances-for-Metagenomic-Binning-with-Right-Skewed-Distribution-Models.

Sickle cell disease (SCD) is the most common inherited blood disorder worldwide. Although monogenic, it presents substantial clinical heterogeneity influenced by genetic modifiers, including haplotypes and fetal hemoglobin (HbF) levels. This pilot cross-sectional study aimed to characterize, for the first time, the βS gene haplotype distribution among Moroccan patients with sickle cell anemia and evaluate its impact on hematological parameters, particularly HbF levels. Eight polymorphic sites within the β-globin gene cluster were analyzed using PCR-RFLP in 334 chromosomes from SCD patients in northern Morocco. Associations between haplotypes and HbF levels were evaluated. PCR RFLP showed that the Benin haplotype was the most common (61.1%), followed by Bantu (14.1%), Atypical A1 (11.7%), Senegal (10.5%), and Arab-Indian (2.7%). The most frequent genotypes were Ben/Ben (41.3%), Ben/CAR (15%), and Ben/Sen (10.2%). HbF levels varied significantly across haplotypes (p < 0.005), with Senegal and Arab-Indian showing the highest levels and Benin and Bantu the lowest. This study highlights both the genetic and anthropological diversity of SCD in Morocco, likely reflecting historical African gene flow. Haplotype profiling enhances understanding of genotype-phenotype correlations, offering valuable insights for prognosis and individualized care strategies to improve patients' outcomes.

The transfer of pesticides to Aiguillon Bay, a major coastal ecosystem on the Atlantic coast of France, was investigated in relation to watershed characteristics, agricultural pressure, and hydrological dynamics. The bay receives inputs from three main rivers (Sèvre Niortaise, Lay, and Curé) as well as from the Vieux channel, a downstream branch of the Lay watershed characterized by distinct land-use and drainage features. This study combined spatial land-use analysis with contamination indicators to clarify pesticide transfer pathways and associated ecological risks in intensively cultivated sub-basins. Monthly surface water samples were analyzed using LC-MS/MS and GC-MS/MS. A Proximity Indicator was developed to identify high-pressure agricultural zones adjacent to watercourses. Individual Risk Quotients (RQs) were also calculated by comparing measured environmental concentrations with Predicted No-Effect Concentrations (PNECs) to evaluate the ecological risk associated with selected pesticide compounds, and the Cumulative Toxic Pressure Index (CTPI) was applied to assess mixture toxicity. CTPI analysis revealed recurrent exceedances of the toxicity threshold (CTPI > 1) across all monitored systems, with strong seasonal variability linked to hydrological conditions. The Sèvre Niortaise and Vieux channel exhibited sustained mixture pressure, whereas the Lay showed pronounced event-driven peaks associated with rainfall episodes. Despite its smaller size, the Curé watershed displayed disproportionately high toxic pressure, reflecting strong hydrological connectivity and cereal-dominated land use. Herbicides and their metabolites were the primary contributors to mixture toxicity, including the persistent metabolite chlorothalonil R471811, frequently detected despite its regulatory ban in 2020, suggesting legacy contamination and progressive remobilization. Although individual Risk Quotients indicated negligible ecological risk for the selected compounds, CTPI revealed repeated mixture toxicity exceedances, demonstrating that cumulative effects represent the primary ecological pressure within the watershed. By integrating land-use characterization, hydrological analysis, statistical comparison, mixture toxicity assessment, and ecological risk evaluation, this study provides a comprehensive framework for understanding pesticide transfer to protected coastal ecosystems and supports the development of more effective watershed management and monitoring strategies.

Nucleotide metabolism is a fundamental biochemical process, providing the building blocks for DNA and RNA synthesis while driving critical cellular functions like energy transfer, signal transduction, and coenzyme synthesis. The precise regulation of nucleotide de novo synthesis, salvage, and degradation pathways is imperative for maintaining genomic stability and tissue homeostasis. Aberrations in these networks are increasingly recognized as primary drivers in various pathologies; notably, cancer cells exploit metabolic-functional reprogramming to enable rapid proliferation and therapeutic resistance. Despite the growing recognition of these metabolic vulnerabilities, an integrated understanding of how specific enzymatic dysregulations translate into diverse disease phenotypes remains fragmented. This review systematically synthesizes the physiological regulatory mechanisms governing nucleotide metabolism and describes the molecular underpinnings of its dysregulation across malignant, immune, and neurodegenerative disorders. We critically examine how specific metabolic enzymes are exploited to drive pathogenesis and highlight the complex interplay between nucleotide metabolites and inflammatory or oncogenic signaling cascades. Furthermore, we evaluate recent clinical innovations in precision medicine, focusing on novel inhibitors targeting key metabolic nodes. By mapping these intricate metabolic networks, this article provides a crucial basis for overcoming current therapeutic challenges, offering profound insights to accelerate the development of next-generation targeted therapies.

Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes, shaping genome structure and evolution; however, their chromosomal distribution and lineage-specific dynamics remain incompletely understood. Here, we analyzed the abundance, spatial organization, and evolutionary history of intact LTR-RTs across 208 plant species using highquality chromosome-level genomes and the MegaLTR tool. Our analyses reveal extensive interspecific variability in LTR-RTs composition and chromosomal organization. Across families, LTR-RTs distributions are significantly non-random, with chromosome identity strongly influencing accumulation patterns. Although both

Acute leukemia (AL) is a malignant hematological disorder, with two main subtypes: acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). The incidence rate of AML and ALL is estimated at approximately 2.7 and 1.5 per 100,000 people, respectively, with an overall mortality rate of approximately 23.6%. This study aimed to investigate the association between human leukocyte antigen (HLA)-C genotypes and AML and ALL in a Moroccan population. A cross-sectional and comparative study was conducted on 100 patients with AL including 43 cases of AML and 57 cases of ALL, compared to 120 healthy individuals as controls. HLA-C genotyping was performed in the two groups, using the PCR-SSO (polymerase chain reaction-sequence-specific oligonucleotide)-based technique. The mean age of the patients was 32 ± 13 (2-62), with a sex ratio of 1.22 (55 male and 45 female patients). In patients with ALL categories, we observed a significantly higher frequency of HLA-C*12 [ Our findings show a strong association between HLA-C*12 and HLA-C*08 allele groups and AL, including both ALL and AML, which gives evidence of a predisposing effect. This highlights the influence of HLA polymorphism in the occurrence or resistance of AL in our population.

The honey wine ( The online version contains supplementary material available at 10.1007/s13197-025-06372-2.

Accurate assessment of disease severity is essential for evaluating fungicide performance and breeding disease-resistant crop varieties. Manual scoring of infection on individual leaf discs is labor-intensive and variable, while traditional computer vision methods require manual parameter tuning and lack robustness. Existing deep learning approaches often struggle to simultaneously localize leaf discs and accurately segment disease symptoms, limiting their practical application. We developed SporaScan, an automated pipeline combining YOLO v8n for leaf disc localization, Mobile SAM for background removal, and UNet for sporulation segmentation. It achieved high accuracy (mAP@50 >99%, mIoU@50 >96%), with background removal reducing misclassification (0.21% for sporulation and 2.75% for leaf discs). Severity estimates showed strong agreement with manual annotations (R These results demonstrate that SporaScan provides an efficient and practical approach for automated assessment of downy mildew severity, supporting applications in disease evaluation, breeding, and fungicide assessment (http://116.10.197.212:9060/segment/#/). © 2026 Society of Chemical Industry.

Bioactive peptides (BAPs) derived from food proteins exhibit a wide range of health-promoting activities, but their potent in vitro bioactivity is disconnected from their often-limited efficacy in vivo. This discrepancy is driven by aggressive gastrointestinal digestion, low epithelial permeability, and rapid systemic clearance. This review assesses the critical role of the food matrix (FM) in regulating peptide bioavailability, addressing the new challenge of overcoming low oral absorption of diverse peptide classes. First, foundational concepts are established, defining the multi-scale nature of FM and the characteristics of BAPs. The physiological barriers to absorption are then detailed, focusing on enzymatic degradation and the mechanisms of transepithelial transport. The core of this review examines the specific molecular interactions between peptides and proteins, lipids, carbohydrates, and polyphenols, showing how they govern stability and bioaccessibility. A comparative analysis of dairy, plant-based, and engineered matrices illustrates how different food structures control release kinetics. Finally, methodologies from in silico prediction to in vivo models are critically evaluated. To solve these delivery challenges, we identify crucial knowledge gaps and suggest future directions, specifically advocating for matrix-engineered delivery systems (such as microencapsulation and probiotic fermentation) to establish a holistic, matrix-aware approach to functional food design. © 2026 Society of Chemical Industry.

Wiskott-Aldrich syndrome (WAS) is a rare X-linked inborn error of immunity characterized by thrombocytopenia, eczema, and recurrent infections, with additional risks of autoimmunity and malignancy. Country-level data from North Africa are scarce. We report the first genetically confirmed Moroccan series of WAS, describing diagnostic pitfalls, clinical spectrum, and molecular findings. We conducted a mixed retrospective-prospective observational cohort study of male patients with molecularly confirmed Wiskott-Aldrich syndrome managed at a Moroccan tertiary referral center between January 2017 and September 2024. Clinical features, hematologic and immunologic data, management, and outcomes were collected from hospital records and available follow-up. Ten male patients were included. Thrombocytopenia was present in all patients (100%), followed by recurrent infections in 9/10 patients (90%) and eczema (90%). Autoimmune complications occurred in 2/10 patients (20%), manifesting as systemic lupus erythematosus with lupus-nephritis-compatible disease in one case and autoimmune hemolytic anemia in the other. Mean platelet volume (MPV) was available in 9/10 patients and was reduced in 2/9 (22.2%). Molecular analysis identified seven distinct pathogenic/likely pathogenic variants: two nonsense (p.Gly322* and p.Arg321*), one splice-site (c.735-2A > T), two frameshift (p.Pro330Leufs*115 and p.Arg431Serfs*64), and two missense (p.Val50Asp and p.Phe128Cys). The p.Gly322* variant recurred in three related patients, including twin brothers, while c.735-2A > T was found in two unrelated individuals, highlighting both familial recurrence and allelic heterogeneity. Truncating and splice-site variants predominated in this cohort (8/10, 80%), consistent with previously reported classic WAS cohorts. One child underwent hematopoietic stem cell transplantation (HSCT) abroad with sustained remission, whereas the others remain on supportive therapy with intravenous immunoglobulin and antimicrobial prophylaxis. This first genetically confirmed Moroccan case series expands the clinical and molecular spectrum of Wiskott-Aldrich syndrome in North Africa. Our findings highlight the marked clinical and genetic heterogeneity of WAS and underscore the importance of early molecular diagnosis to guide appropriate management, genetic counseling, and timely referral for curative therapy in resource-limited settings.