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Review
Biology and Life Sciences
Biology and Biotechnology

Damaris G. Nieva-Ramírez

,

David Luna-Pérez

,

Misael Uribe

,

Natalia Nuño-Lámbarri

Abstract: Breast cancer remains the most frequently diagnosed malignancy among women worldwide, while metabolic dysfunction–associated steatotic liver disease (MASLD) represents the leading cause of chronic liver disease, reflecting a global burden of metabolic dysfunction. Increasing evidence suggests that MASLD is not only a common comorbidity but also a potential independent risk factor for breast cancer development and progression. This review synthesizes current epidemiological, clinical, and mechanistic data linking hepatic metabolic dysfunction to breast carcinogenesis. Population-based studies consistently demonstrate an association between hepatic steatosis and increased breast cancer incidence, particularly in postmenopausal and metabolically vulnerable populations, as well as poorer oncological outcomes. Mechanistically, MASLD promotes a systemic pro-tumorigenic environment through interconnected pathways, including insulin resistance, hormonal dysregulation with increased estrogen bioavailability, chronic inflammation, oxidative stress, lipid metabolic reprogramming, and gut–liver axis disruption. Hepatokines, particularly fibroblast growth factor 21 (FGF21), emerge as key mediators of tumor progression and potential biomarkers of metabolic vulnerability, while Fetuin-A and ANGPTL8 further support the liver’s endocrine role in oncogenic signaling. Preclinical evidence highlights fatty acid oxidation as a metabolic dependency in aggressive breast cancer subtypes, suggesting novel therapeutic targets. Despite consistent associations, causality remains unproven. Future prospective studies are needed to determine whether targeting metabolic dysfunction can improve breast cancer prevention and outcomes.

Review
Biology and Life Sciences
Biology and Biotechnology

Israr Khan

,

Fazal Akbar

,

Mohammad Ali

,

Syed Shujait Ali

,

Zafar Ali

,

Arshad Iqbal

,

Shahid Ali

,

Nisar Ahmad

,

Muhammad Nazir Uddin

Abstract: The increasing burden of municipal solid waste, petroleum hydrocarbons, industrial wastewater, saline soils, marine pollution, electronic wastes, and plastic contaminants is among the foremost global environmental issues that need sustainable remediation practices. In this review, the current status and future prospects in terms of the use of bioremediation techniques for environmental remediation are highlighted by discussing their advancements over the years 2020–2026. Various in situ and ex situ remediation techniques like bioaugmentation, biostimulation, biosparging, land farming, composting, bioreactor techniques, phytoremediation, activated sludge process, algal remediation, and fungal-based remediation techniques are highly efficient for the degradation of hydrocarbons, dyes, pharmaceutical compounds, heavy metals, volatile organic compounds, and new-age plastic pollutants. Microbial genera such as Pseudomonas, Bacillus, Alcanivorax, Aspergillus, Trametes, and halotolerant plant growth-promoting rhizobacteria exhibit an important role in pollutant mineralization, transformation, and detoxification through different metabolic pathways and enzyme systems. Emerging developments in synthetic biology, AI-assisted waste management, engineering of microbial consortia, and circular bio-economy models have enhanced the efficiency of remediation processes. Nonetheless, problems associated with scale-up, environmental variability, pollutant complexity, cost-effectiveness, and incomplete mineralization hinder practical application in field conditions.

Article
Biology and Life Sciences
Biology and Biotechnology

Paula Reul

,

Simone Schweda

,

Joana Schmidt

,

Andreas M. Niess

,

Inga Krauss

,

Barbara Munz

Abstract: (1) Background: The MultiPill-Exercise study was an exercise-based lifestyle intervention program for subjects with more than one lifestyle-related disease. Metabolomics-based approaches are an emerging tool in sports medicine, both in basic science and in clinical contexts. In this explorative, hypothesis-generating study, we aimed at defining metabolite patterns in subjects with multimorbidity and to test the predictive value of metabolite patterns for fitness adaptation. (2) Methods: A targeted tandem mass spectrometry (MS) approach on dried spots of capillary blood was employed, analyzing n = 86 subjects. (3) Results: In response to an acute bout of exhaustive exercise, aromatic amino acids (AA) tyrosine (Tyr) and phenylalanine (Phe), total carnitine (Cx) and short- as well as medium-chain acylcarnitines (SCA and MCA) were upregulated. Furthermore, concentrations of most metabolites were higher in males. Multiple regression defined free carnitine (C0), MCA and MCADelta, i.e. changes in concentrations during acute exercise, as important predictors of intervention-associated fitness adaptation after six months, explaining 24.8% and 24.4% of absolute and relative power gains associated with a respiratory quotient (RQ) of 1, a submaximal fitness parameter. (4) Conclusions: Our data suggest utility of metabolomics data in subjects with multimorbidity, both in the context of basic research and clinical applications.

Article
Biology and Life Sciences
Biology and Biotechnology

Hilda Mabel Sosa-Esquivel

,

Atzin Fraire-Mayorga

,

Yadira Yumiko De la Cruz-Rodríguez

,

Angélica Judith Granados-López

,

Gloria Viviana Cerrillo-Rojas

,

Jesús Adrián López

,

Saúl Fraire-Velázquez

Abstract: Bacillus velezensis is a rhizosphere-associated bacterium widely recognized for its roles in biological control and plant growth promotion; however, its functional diversity and evolutionary structure across scales remain incompletely understood. This study evaluated strains 2A-2B, 3A-6A, 2A-10A and 3A-25B from the Center-North of Mexico through integrated phenotypic assays and comparative genomics. Antagonistic activity was assessed via dual confrontation assays against major chili pepper phytopathogens, and plant–bacteria compatibility was examined in vitro. Genome-based analyses included pan-genome reconstruction, phylogenetic inference, and functional annotation, incorporating the screening of plant-associated genetic traits using the PLaBAse platform. All strains consistently inhibited phytopathogens (40–80%), with no significant differences among them, and displayed non-pathogenic interactions with the host plant. Genomic analyses revealed highly conserved core features alongside variation in accessory and strain-specific genes, with strain 3A-25B showing the highest divergence. Pan-genome analyses at regional and global scales indicated an open structure shaped by geography. Phylogenetically, three strains clustered together, whereas strain 3A-25B grouped with distant lineages. All genomes encoded extensive plant growth–promoting traits, while a substantial fraction of genes remained unannotated. These findings highlight functional consistency despite genomic divergence and support the ecological versatility and biotechnological potential of native B. velezensis strains.

Article
Biology and Life Sciences
Biology and Biotechnology

Ana Guadalupe Castillo-Olmos

,

Abigail Varela-Pérez

,

Hugo S. García-Galindo

,

Joaquín A. Quiroz-Mercado

,

Kimberly Castañeda-Gutiérrez

,

Carlos Amero-Tello

,

Enrique Rudiño-Piñera

,

Mizraim Morales-Mendoza

,

Cynthia Cano-Sarmiento

Abstract: Cataracts are the leading cause of reversible blindness worldwide, this condition results from the aggregation of lens proteins. Currently, surgery remains the only effective treatment; however, there is growing interest in non-surgical approaches, including the use of bioactive compounds incorporated into nanostructured delivery systems designed to enhance solubility, enable controlled release, and improve bioavailability and bioactivity. Among the bioactive compounds investigated, curcumin has attracted considerable attention due to its antioxidant and anti-inflammatory properties, positioning it as a potential anticataractogenic agent. In the present study, a curcumin-loaded nanoemulsion was developed via ultrasonication and characterized in terms of average particle size, D90 percentile, ζ potential, temporal stability, and rheological behaviour. In addition, its anti-cataract efficacy was evaluated both using an in vivo model in rats and an ex vivo model employing human cataract samples. The resulting curcumin-carrying nanoemulsion exhibited an average particle size of 152 ± 19.79 nm with a monomodal distribution, along with good physical stability over time. On the other hand, the nanoemulsion exhibited viscosity values of 31.36 ± 1.88 to 25.96 ± 0.81 mPa·s and a near Newtonian flow behavior. Regarding the effect on cataracts, in the in vivo model, cataract reversal of at least two grades was observed. Furthermore, ex vivo isothermal titration calorimetry analyses confirmed exothermic binding interactions between the curcumin nanoemulsions and cataract fragments, suggesting the involvement of multiple binding sites within lens components, most likely crystallin proteins. These findings support the potential of curcumin-based nanoemulsions as promising therapeutic candidates for the treatment of cataracts.

Review
Biology and Life Sciences
Biology and Biotechnology

Olanrewaju B. Morenikeji

,

Marvellous Agbanusi

,

Oluwatobi Fijabi

,

Muyiwa S. Adegbaju

,

Kyra A. Baker-Waters

,

Maneiqua C. Marshall

,

Prakash K. Singh

,

Xiomara Lane

,

Adeola Ayoola

,

Adedeji O. Adetunji

+7 authors

Abstract: MicroRNAs (miRNAs) are evolutionarily conserved, ~22-nucleotide non-coding RNAs that orchestrate post-transcriptional gene silencing across virtually all metazoan lineages. Since the landmark discovery of lin-4 in Caenorhabditis elegans over three decades ago, the miRNA field has expanded to encompass more than 2,600 annotated human miRNAs collectively targeting over 60% of protein-coding genes, establishing miRNAs as master regulators of cellular homeostasis, differentiation, and stress adaptation. This review articulates a conceptual framework positioning miRNAs as integrative molecular nodes at the intersection of two fundamental biological processes: the heat shock response (HSR) and host immunity. We synthesize evidence demonstrating that thermal stress, whether arising from environmental hyperthermia, febrile immune responses, or climate-driven ecological perturbation, profoundly reshapes miRNA biogenesis, stability, and target engagement, with cascading consequences for innate and adaptive immune signaling. Mechanistically, we trace how heat shock factor 1 (HSF1) undergoes temperature-dependent liquid–liquid phase separation to activate transcription of heat shock proteins (HSPs) and specific miRNA loci, generating feedback circuits that calibrate inflammatory tone through NF-κB, TLR, and inflammasome pathways. Multi-omics integration including transcriptomics, proteomics, metabolomics, and small RNA sequencing has revealed a systems-level "regulatory flux" in which miRNAs dynamically buffer cellular responses to concurrent thermal and immunological challenges. We further examine how pathogens exploit and subvert host miRNA circuits during infection, and how extracellular vesicle-mediated miRNA transfer enables intercellular and inter-organ stress communication. Finally, we survey the translational horizon, including miRNA mimics, antagomiRs, engineered delivery systems, and synthetic miRNA circuits, highlighting both therapeutic promise and outstanding challenges. By reframing miRNAs as rheostatic integrators bridging stress physiology and immunology, this review establishes a foundation for interdisciplinary research at the thermal stress–immunity nexus.

Review
Biology and Life Sciences
Biology and Biotechnology

Rajani Singh

,

Shilpa Mohanty

,

Suneel Kateriya

Abstract: In recent decades, the evolution of optogenetic engineering has revolutionised biomedical (neuroscience) research and synthetic biology. It also opens exciting opportunities in the biomanufacturing sector, paving the way for opto-biotechnology, a light-driven system for scalable production of valuable products. This review consolidates the evolution of optogenetics into opto-biotechnology across pharmaceuticals, nutraceuticals, lipids, antibodies and biofuels. Here, we highlight conceptual designs for opto-biotechnology in scalable biomanufacturing as the next frontier beyond optogenetics and as a clue to the synthesis of light-driven biosynthetic gene clusters mediated bioactives. It will also discuss how opto-biotechnology intersects with synthetic biology, systems biology, and bioprocess engineering to push the frontiers of programmable biomanufacturing without genetic interventions. Moreover, moving forward to translational application, as future strategists, we will discuss the integration of machine learning, computational modelling and artificial intelligence for crafting the precise light exposure tactics and factors, increasing the yield and efficiency of opto-modulated systems, thereby reshaping the landscape of optobiomanufacturing.

Article
Biology and Life Sciences
Biology and Biotechnology

Mihaela Afrodita Dan

,

Emma Adriana Ozon

,

Denisa Margină

,

Marina Ionela Nedea

,

Claudia Maria Guțu

,

Anca Ungurianu

,

George Mihai Nitulescu

,

Violeta Popovici

,

Adina Magdalena Musuc

,

Veronica Bratan

+6 authors

Abstract: Plant extracts in vegetable oils are foundational and eco-responsible for skin care, act-ing as potent antimicrobials, antioxidants, photoprotectants, and emollients. The pre-sent research aims to conduct a comprehensive investigation of Usnea barbata extract in Karanja oil (KO). The lichen extract (UBKO) was obtained through cold maceration. Phytochemical screening was performed using the Folin-Ciocalteu method and Graphite Furnace Atomic Absorption Spectrophotometry (GFAAS). Physicochemical properties were evaluated by Atomic Force Microscopy (AFM) and Fourier Transform Infrared Spectroscopy (FTIR). The rheological characteristics and oxidative resistance of both oil samples, with and without U. barbata (UBKO and KO), were investigated. The bioactive potential of UBKO was assessed by evaluating antioxidant properties, sunscreen efficacy, and antibacterial and antifungal activity. UBKO had a slightly lower density (0.827 vs. 0.955) and pH (4.22 vs. 4.86) than KO, and a slightly higher oxidative resistance, quantified as the induction period (IP) value (6.45 vs. 6.00). The total phenolic content was significantly greater in UBKO than in KO (567.16 ± 14.96 vs. 433.26 ± 22.96 mg GAE/mL, p < 0.05). The antibacterial effect against S. aureus was higher for UBKO than KO (25 ± 0.00 vs. 31.25 ± 18.75 mg/mL, p < 0.05), while the in-hibitory activity of UBKO against C. albicans was considerably higher than that of KO (6.75 ± 0.00 vs. 37.50 ± 12.50 mg/mL, p < 0.05). Finally, our results showed that UBKO had an appreciable sun-protective factor (SPF) slightly higher than KO (30.9 vs. 29.8). Therefore, our study suggests that U. barbata extract in Karanja oil could be used to develop pharmaceutical formulations with antimicrobial and photoprotective effects, with potential applications for skincare.

Review
Biology and Life Sciences
Biology and Biotechnology

Prachi Agrawal

,

Salil Tiwari

,

Prachi Mendhey

,

Preethi Jampala

,

Harish Rajak

,

Nawneet Kurrey

,

Neesar Ahmed

,

Sandeep K. Yadav

,

Santosh Kumar

Abstract: Intercellular mitochondrial trafficking has emerged as an important mechanism influencing tumor progression, metabolic adaptability, and cancer cell plasticity. Beyond their classical bioenergetic functions, mitochondria act as central regulators of redox homeostasis, signalling pathways, and epigenetic remodelling. Increasing evidences suggest that mitochondria can be transferred between tumor, stromal, and immune cells through tunnelling nanotubes (TNTs), extracellular vesicles (EVs), gap junctions, and cell fusion within the tumor microenvironment. This dynamic exchange enables metabolically compromised cancer cells to restore oxidative phosphorylation, optimize energy production, and survive under hypoxia and therapeutic stress. Mitochondrial transfer has been increasingly associated with enhanced cellular plasticity and adaptive phenotypic transitions, including the acquisition of stem-like features that contribute to tumor heterogeneity, metastasis, and treatment resistance. In addition to bioenergetic restoration, transferred mitochondrial DNA and metabolites participate in retrograde signalling, linking metabolic state to epigenetic regulation and transcriptional reprogramming. This metabolic epigenetic interplay supports tumor cell adaptation to environmental stress and therapeutic pressure. Although significant progress has been made, the precise mechanisms governing mitochondrial integration and their long-term impact on cellular phenotypes remain incompletely understood. A deeper understanding of these processes may reveal new therapeutic strategies to disrupt tumor adaptability and improve treatment outcomes.

Article
Biology and Life Sciences
Biology and Biotechnology

Matthew Chadwick

,

Maria Sole Regina Lancerin

,

Patricia Hazelton

,

Kyriakos Vidalis

,

Emmanuel Petit

,

Paolina Lukova

,

Cédric Delattre

,

Xianfeng Chen

,

Thamarai Schneiders

,

Vasso Makrantoni

+2 authors

Abstract: Fucoidan is a sulfated polysaccharide derived from brown seaweed, reported to possess diverse biological activities that make it a molecule of great interest for nutraceutical and biomedical applications. A significant challenge to its wider implementation is a lack of understanding of the relationship between fucoidan’s structural and chemical characteristics with biological activity. So far, approaches to identifying these relationships have been limited to qualitative comparisons of chemical and biological datasets or producing unnatural modified fucoidans through chemical methods. This work aimed to apply a formalized methodology to elucidate potential relationships worthy of further exploration. The biological activity of commercial fucoidan extracts that had undergone a detailed chemical characterization process was assessed. The extracts exhibited multiple bioactivities, notably antioxidant activity, antiviral activity against Nipah virus, antifungal activity against Candida dubliensis and prebiotic effects on Lactobacillus casei. With no antifungal activity against Candida albicans, Candida auris and Cryptococcus neoformans, nor antibacterial effects against Klebsiella pneumoniae. Correlation analysis of biological activity and extract chemical characterization data identified several potential key quality attributes. With high fucose content, high sulphate content identified as potentially important for antioxidant, antiviral, antifungal, and prebiotic activities. This work addressed literature’s debate regarding the optimal molecular weight for bioactivity, suggesting that it depends on the specific microbe to which a fucoidan extract is applied.This study demonstrated that a formalized comparative approach, linking chemical and structural data with biological activity, can effectively identify important characteristics of fucoidan for a specific bioactivity that requires further exploration. Future work should focus on expanding this approach, measuring the bioactivity of more chemically characterized fucoidans against more microbes. Additionally, extracts possessing identified quality attributes should be produced and employed in mechanistic studies to further validate the correlations drawn in this work.

Review
Biology and Life Sciences
Biology and Biotechnology

Mehran Khorshid

,

Zahra Alizadeh Khatibani

,

Ehsan Pashay Ahi

Abstract: Environmental RNA (eRNA) has been increasingly used to move beyond “who is there” toward “who is active” and “what is happening” in ecosystems. Yet, most workflows have been optimized for laboratory sequencing, and decision-grade field use has remained sporadic. In this article, field-ready eRNA panels are defined as curated sets of transcripts paired with process controls and a transparent scoring rule, and a build–test pathway is described from marker discovery to deployment. Candidate markers are prioritized with field constraints in mind (abundance, specificity, persistence, and confounding seasonality), and RNA class choice (mRNA, rRNA, small and other non-coding RNAs) is treated as a design lever for robustness. Pre-analytics are discussed as panel engineering, with emphasis placed on capture, rapid stabilization, and inhibitor management to preserve multi-marker relationships. Field readout options are then compared, including isothermal amplification, CRISPR-assisted detection, portable qPCR, and portable nanopore sequencing for on-site verification and panel refresh. Finally, minimum controls and staged validation levels are proposed to support defensible ecological claims. Deliberate attention is directed toward shared terminology and testable standards so that discussion within and between ecology, diagnostics, and conservation practice is stimulated and priorities for future investigations are sharpened.

Review
Biology and Life Sciences
Biology and Biotechnology

Victoria Sherwood

,

Denise Harold

,

Richard O’Kennedy

,

Christine Loscher

,

Paul Leonard

Abstract: Monoclonal antibody (mAb) discovery has been transformed by advances in single-cell technologies, microfluidics, high-throughput sequencing, and computational design. Modern platforms enable the interrogation of large numbers of individual B cells, directly linking antibody sequence with antigen specificity and functional activity. Microfluidic and optofluidic systems now support high-throughput compartmentalisation and functional screening of antibody-secreting cells, while sequencing-based approaches allow parallel recovery of paired heavy- and light-chain sequences. These developments have shifted antibody discovery from binding-based selection toward function-first paradigms, enabling the rapid identification of diagnostic and therapeutically relevant antibodies. Integration with computational tools, including machine learning and structure-based modeling, has further enabled the emergence of closed-loop discovery pipelines, in which experimental and in silico methods iteratively refine candidates. This review summarises key advances in single-cell microtools over the last decade and highlights how the convergence of experimental and computational technologies is reshaping antibody discovery toward scalable, data-driven, and increasingly automated platforms.

Article
Biology and Life Sciences
Biology and Biotechnology

Bruno H. de Oliveira

,

Valéria M. G. do Nascimento

,

Maria de Lourdes T. M. Polizeli

Abstract: The transition toward sustainable biorefinery processes requires efficient strategies for lignocellulosic biomass deconstruction and valorization. In this study, an integrated enzymatic system combining fungal holocellulases and laccases with a bacterial galactolipase was developed and evaluated. The consortium, composed of Trametes hirsuta GMA-01, Mycothermus thermophilus CBS 619.91, and Burkholderia lata BL02, was produced using agro-industrial substrates and applied to the hydrolysis of different lignocellulosic biomasses. The incorporation of galactolipase activity enhanced saccharification yields for leaf-derived substrates, reaching up to 292.0 mg/g for spinach leaves and 236.0 mg/g for corn straw, compared to fungal systems alone. This effect is associated with the selective hydrolysis of membrane-associated galactolipids, improving substrate accessibility to holocellulolytic enzymes. Proteomic analysis and structural modeling identified the BL02 enzyme as a versatile ester hydrolase with features compatible with accommodating bulky polar substrates. In addition, the enzyme catalyzed the synthesis of sugar fatty acid esters with conversion yields above 50% for glucose and xylose in binary solvent systems. These findings support the role of galactolipases as accessory enzymes and highlight their potential application in integrated and sustainable biorefinery processes.

Article
Biology and Life Sciences
Biology and Biotechnology

Kentaro Yamada

,

Nicholas Campbell

Abstract: The integration of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy holds great promise for comprehensive biomolecular profiling, yet existing computational approaches are limited to single modality analysis, employ static fusion strategies, and incur prohibitive inference costs. We propose SpectraLLM, a unified large language model-driven framework for multi-modal biological spectrum analysis. SpectraLLM introduces a modality-agnostic spectral encoder that projects both MS and NMR spectra into a shared token space, a contribution-aware dynamic multi-modal balance mechanism that adaptively weights each modality per sample, a flow-based knowledge distillation strategy that compresses the teacher model to a compact student with 4.3× lower latency, and parameter-efficient transfer learning via lightweight adapters for rapid domain adaptation. Evaluated on three large-scale benchmarks—MetaboSpectrum-10K, ProteinSpectra-5K, and CellNMR-3K—SpectraLLM achieves state-of-the-art performance, including an AUC of 0.947 for biomarker identification and 96.1% teacher performance retention after distillation. In a clinical case study on early-stage pancreatic cancer detection, SpectraLLM achieves an AUC of 0.961, substantially outperforming both the clinical standard CA 19-9 and existing computational methods, demonstrating the potential of LLM-driven multi-modal spectral analysis for precision medicine.

Review
Biology and Life Sciences
Biology and Biotechnology

Yusuf Bozkurt

,

Marcia Saraiva

,

Rigers Bakiu

,

Vladamir Radosavljevic

,

Carla O Silva

,

Perveen Akhtar

,

Stojmir Stojanovski

,

Dijana Blazhekovikj-Dimovska

,

Ari Meerson

,

Ivana Giovanna Zupičić

Abstract: Aquaculture in Europe has experienced significant growth in recent decades, driven by rising demand for sustainable production and strong policy frameworks promoting environmentally responsible aquaculture practices. Biomarkers, defined as measurable biological indicators reflecting physiological, biochemical, or molecular responses to environmental and biological stressors, have greatly expanded their use in aquaculture applications. In this regard, biomarker-based approaches are increasingly applied in multiple areas of aquaculture, including health and disease monitoring, welfare as-sessment, environmental toxicology, reproductive biology, population management, and the optimization of cryopreservation protocols. This review provides a compre-hensive overview of current biomarker applications in European aquaculture, highlig-hting recent technological advances, methodological challenges, and emerging rese-arch directions. By synthesizing current knowledge and identifying future research priorities, this review aims to contribute to the development of biomarker-driven mo-nitoring strategies that enhance the resilience, efficiency, and sustainability of aqua-culture in Europe.

Review
Biology and Life Sciences
Biology and Biotechnology

David Gramaje

,

Ales Eichmeier

Abstract: Esca remains one of the most conceptually challenging disease syndromes of grapevine because it cannot be reduced to a single pathogen, lesion type or external phenotype. Foliar symptoms are erratic, internal wood damage is heterogeneous, and fungi associated with the syndrome may persist in asymptomatic vines. Much of this difficulty stems from treating esca-associated fungi as functionally equivalent, even though they occupy different niches and contribute differently to disease development. Here, we revisit grapevine esca through a fungal-biology-centred framework focused on Phaeomoniella chlamydospora, Phaeoacremonium minimumand white-rot basidiomycetes, especially Fomitiporia mediterranea. We argue that the esca pathosystem is best understood as the interaction between two biologically connected but non-equivalent fungal layers: a pioneer vascular phase and a later white-rot phase. Within this perspective, Petri disease and esca proper are interpreted as stages along a continuous host-fungus trajectory shaped by colonization strategy, tissue occupation, decay biology and pathobiome context. This distinction clarifies why host phenotypes are so difficult to interpret. Current evidence supports partially independent layers of host response, including resistance to pioneer colonization, tolerance to hydraulic dysfunction, resistance to wood decay and resilience under chronic infection. We therefore propose that “esca resistance” should be interpreted not as a unitary host trait, but as a multidimensional consequence of fungal functional differentiation, host physiology and environmental modulation.

Article
Biology and Life Sciences
Biology and Biotechnology

Renfeng He

,

Wei Liu

,

Xiaotong Shao

,

Zejiang Zhu

,

Keke Sun

,

Yuwan Liu

,

Huifeng Jiang

,

Dingyu Liu

Abstract:

Microbial protein production from acetate represents a promising route for sustainable protein supply, yet its efficiency is constrained by limited understanding of carbon–nitrogen metabolic coordination. In this study, nitrogen availability was systematically varied to investigate its role in regulating carbon partitioning and protein biosynthesis in Yarrowia lipolytica. Nitrogen limitation markedly reduced cell growth and protein accumulation (19.56% of dry cell weight) while increasing lipid content (up to 34.16%), indicating a redistribution of carbon flux from protein to lipid synthesis. Transcriptomic analysis revealed a global downregulation of anabolic pathways under nitrogen limitation, accompanied by a shift in nitrogen assimilation from the glutamate dehydrogenase (GDH) pathway to the glutamine synthetase/glutamate synthase (GS–GOGAT) pathway, as well as significant upregulation of genes related to ammonium and amino acid transport. Guided by these findings, metabolic engineering of key nitrogen assimilation pathways was performed. Co-overexpression of GDH and GS increased protein content from 48.52% to 55.77% and improved amino acid composition, whereas GOGAT overexpression impaired growth and protein accumulation. These results demonstrate that nitrogen availability governs carbon allocation through coordinated regulation of nitrogen transport and assimilation, and that balanced enhancement of GDH and GS is an effective strategy to improve protein production from acetate, supporting the development of sustainable fermentation processes using CO₂-derived substrates.

Article
Biology and Life Sciences
Biology and Biotechnology

Muhammad Shoaib Akhtar

,

Mian Sahib Zar

,

Abdul Rehman Haris

,

Samia Tahir

Abstract: Polymerase chain reaction (PCR) is a widely used molecular biology technique; however, it remains highly susceptible to non-specific primer binding, particularly in genomic regions with extensive sequence similarity. Such off-target amplification can generate false amplicons that are difficult to detect using conventional quality control methods and may lead to erroneous downstream interpretation. Here, we present FalseAmpHunter, a pipeline designed to detect, assemble, and characterize false amplicons from paired-end next-generation sequencing (NGS) data generated from PCR amplification. FalseAmpHunter reconstructs candidate amplicons, maps them genome-wide, evaluates primer-binding orientation, and distinguishes true target amplification from paralog-driven off-target products and sequencing artifacts. We validated FalseAmpHunter using a synthetic dataset derived from in silico PCR of paralogous olfactory receptor (OR) genes. The pipeline successfully identified both the intended target amplicon and false amplicons originating from paralogous loci, while excluding a random decoy control. FalseAmpHunter provides a systematic and transparent solution for investigating false PCR amplification events and is applicable to assay development, primer validation, and troubleshooting of targeted sequencing experiments. By transforming raw sequencing data into interpretable genomic evidence, it enhances confidence in PCR-based analyses, particularly in paralog-rich genomic contexts. The pipeline is accessible online at: https://github.com/xoaib4/FalseAmpHunter.

Article
Biology and Life Sciences
Biology and Biotechnology

Andrea Cavagnino

,

Olivier Gouin

,

Maïwenn Campeaux

,

Mike Amzallag

,

Joël Aknin

,

Julien Demaude

,

Raphaël Aknin

,

Martin Baraibar

Abstract: This study supports the use of human skin explants as a versatile and translational model for evaluating pharmacologic skin responses and topical bioactivity. The approach allows mechanistic insight beyond single biomarkers and may serve as a scalable pharmacologic platform for efficacy testing, particularly when expanded to include multiple donors and broader readouts.

Article
Biology and Life Sciences
Biology and Biotechnology

Wenjing Cui

,

Zhi Yang

,

Xuhui Meng

,

Xiaoyan Wang

,

Wenhao Chen

Abstract: (Background) Aiming to reduce synthetic fertilizer dependence and enhance soil fertility, this study isolated and characterized nitrogen-fixing bacteria from the maize rhizosphere. (Methods) Nitrogen-free selective media were used for bacterial isolation, followed by detection of the nifH gene and nitrogenase activity. Phylogenetic identification was conducted via 16S rRNA sequencing. Growth-promoting traits, stress tolerance, and pot-based plant inoculation effects were assessed. Genetic modification of strain GN8811 was performed to improve nitrogen fixation and growth promotion. (Results) Seven isolates that carried the nifH gene and exhibited nitrogenase activity were closely related to four genera. Several isolates showed phosphate solubilization, iron chelation, IAA production, or potassium solubilization, with GN2003 and GN8811 tolerating high salinity and variable pH. Inoculation with GN8811 promoted maize growth comparable to nitrogen fertilization, and its genetically modified derivative (ΔnifL::PrpoD) showed further improvement even under high nitrogen conditions. (Conclusions) These findings highlight the potential of combining microbial screening with genetic engineering to develop efficient bioinoculants for sustainable maize cultivation.

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