Progress in molecular and subcellular biology最新文献

{"title":"Repair of Corneal Epithelial Defects.","authors":"Mark Rabinovich, Elsa W Böhm, Yue Ruan, Adrian Gericke","doi":"10.1007/978-3-032-17771-1_5","DOIUrl":"10.1007/978-3-032-17771-1_5","url":null,"abstract":"<p><p>The corneal epithelium, a stratified squamous non-keratinized layer of 50-60 μm thickness, forms the outermost barrier of the cornea and provides both optical clarity and protection against trauma, infection, and fluid imbalance. It plays a vital role in protecting the eye and maintaining visual clarity. A range of conditions, including trauma, metabolic disorders, microbial infection, and limbal stem cell deficiency, can lead to chronic corneal epithelial defects and subsequent visual impairment. Epithelial renewal is a continuous process, primarily sustained by stem cells located at the limbus. These stem cells give rise to transient amplifying cells, which migrate centripetally and superficially to maintain epithelial integrity. Wound healing follows a highly regulated sequence, superficial cells slide to cover the defect, basal cells proliferate, and corneal nerves realign to support epithelial stratification. This process is orchestrated by cytoskeletal remodeling, integrin-matrix interactions, and growth factor signaling. The epithelium relies on glucose from the corneal stroma, primarily metabolized through glycolysis, while mitochondrial oxidative phosphorylation generates the ATP required for repair. Thus, epithelial regeneration is closely tied to cellular energy availability. Enhancing this process involves supporting mitochondrial function, metabolic signaling pathways, and stem cell activity. Emerging strategies in regenerative ophthalmology include NAD⁺ replenishment, activation of AMP-activated protein kinase (AMPK), application of growth factors, targeted nanotherapies, and photobiomodulation. This chapter explores these cutting-edge approaches aimed at promoting energy-driven regeneration of the corneal surface.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"63 ","pages":"155-174"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147284975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial Biotechnology in Agriculture.","authors":"Mustafa Çilkiz","doi":"10.1007/978-3-032-11438-9_8","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_8","url":null,"abstract":"<p><p>Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"251-306"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147514460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial Metabolism: Primary and Secondary Metabolites.","authors":"Nazmiye Ozlem Sanli, Elif Özlem Arslan Aydoğdu","doi":"10.1007/978-3-032-11438-9_4","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_4","url":null,"abstract":"<p><p>Microbial metabolism encompasses the biochemical networks that enable cells to convert nutrients into the energy and biosynthetic precursors necessary for cellular function. Understanding microbial metabolism is crucial for ecology, microbiology, and applications in biotechnology, agriculture, and medicine, as it underpins the biological processes that sustain life in various environments. Microbial metabolic products can be broadly classified as primary or secondary metabolites. Primary metabolites, such as amino acids, carbohydrates, organic acids, and alcohols, are essential for energy generation, biosynthesis, and cellular maintenance, typically accumulating during the exponential growth phase. In contrast, secondary metabolites, including compounds such as antibiotics, toxins, and alkaloids, are predominantly synthesised during the stationary growth phase and are not essential for basic cellular functions. However, they are often involved in ecological interactions and may provide adaptive advantages to the organisms. This distinction emphasises the dual function of microbial metabolism in supporting life and influencing ecological processes. The regulation of microbial metabolite biosynthesis is influenced by nutrient availability, environmental stresses, and intricate genetic networks. Advances in metabolic engineering, synthetic biology, and CRISPR-based technologies have enabled the redirection of central carbon fluxes to enhance the yield of both primary and secondary metabolites. Multi-omics approaches and computational modeling now provide deeper insights into metabolic regulation, pathway optimization, and the discovery of novel bioactive molecules. In conclusion, microbial metabolites are an invaluable resource for biotechnological innovation. While primary metabolites are essential for metabolic physiology, secondary metabolites offer unique bioactivities that have transformed pharmaceutical development, sustainable agriculture and industrial microbiology. Research focusing on uncovering new microbial diversity and optimising biosynthetic pathways is expected to continue providing insights that could deliver sustainable strategies and innovative solutions to urgent global challenges such as food security, healthcare, and environmental restoration.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"135-162"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147512906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of Archaea.","authors":"Ayten Kimiran, Merve Mücahide Çağ, Nihal Doğruöz Güngör","doi":"10.1007/978-3-032-11438-9_3","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_3","url":null,"abstract":"<p><p>Archaea are prokaryotes that represent a unique evolutionary lineage distinct from bacteria and eukaryotes. Once thought to exist only in extreme environments, archaea inhabit a wide range of habitats, including soil, marine environments, and the digestive systems of living organisms. This section highlights the systematic diversity of archaea, particularly the superphyla Euryarchaeota, TACK, DPANN, and Asgard, along with their respective phyla. Additionally, the ecological distribution of archaea, their morphological and structural differences, their extensive metabolic properties, and their adaptation mechanisms in extreme conditions are discussed to highlight their biological importance and contribute to our understanding of life on our planet.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"93-134"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147514394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mucosal Wound Repair: Reinforcement of Respiratory Mucus Barrier Function by Inorganic Polyphosphate.","authors":"Xiaohong Wang, Heinz C Schröder, Meik Neufurth, Werner E G Müller","doi":"10.1007/978-3-032-17771-1_6","DOIUrl":"10.1007/978-3-032-17771-1_6","url":null,"abstract":"<p><p>Epithelial cell damage affects not only the skin, which covers the external surface of the human body, but also the non-keratinized epithelia, the mucosa, that lines the surfaces of internal organs, including the nasopharynx and lungs. This mucosa is characterized by a moist surface formed by the mucus overlying the epithelial cells. In the respiratory tract in particular, mucosa cells are constantly exposed to large amounts of environmental pathogens and stressors, including bacteria and viruses inhaled as aerosols. Therefore, mucins, a group of glycoproteins that constitute a major component of the mucus, play an important role in the innate immune defense provided by the protective mucus shield. This barrier function of the mucus can be disrupted by a number of agents, such as fine dust (particulate matter). Recent results have shown that inorganic polyphosphate (polyP), which can be administered, for example, in the form of a nasopharyngeal spray, offers a promising way to strengthen or repair impaired mucus function. This chapter describes the structure and formation of the mucus and its mucin building blocks, as well as the mode of action of polyP and drug-loaded polyP nanoparticles in restoring the mucus barrier, particularly with regard to their protective function against coronavirus infection.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"63 ","pages":"175-207"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147284946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota and Microbiome.","authors":"Ozgenur Hacioglu","doi":"10.1007/978-3-032-11438-9_9","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_9","url":null,"abstract":"<p><p>The human microbiota represents a complex and dynamic ecosystem composed of microorganisms from various taxonomic groups, including bacteria, viruses, fungi, archaea, and protozoa. These microorganisms inhabit different anatomical regions of the human body, such as the genitourinary system, the gastrointestinal tract, the oral cavity, the skin, and the respiratory tract, exhibiting distinct densities, compositions, and functional characteristics, and interact reciprocally with the host organism. The term microbiota not only defines the diversity and abundance of microorganisms but also encompasses their functional influence on host physiology. At this point, the concept of the microbiome becomes relevant. The microbiome refers to the collective genomic content of all microorganisms comprising the microbiota, that is, their genetic material and the potential biological functions encoded by their genes. Therefore, microbiome analysis enables not only the assessment of microbial diversity, but also of metabolic capacity, signal transduction, immune regulation, and other host-microbe interactions. The microbiota and microbiome play important roles in preserving human health and homeostatic balance. A healthy microbial composition promotes immune system development, aids digestion and nutrient absorption, reduces pathogenic microorganism colonization, and contributes to the integrity of the mucosal barrier. In contrast, dysbiosis, or disruption of microbial equilibrium, has been linked to a variety of pathophysiological illnesses, including inflammatory diseases, metabolic disorders, neurodegenerative diseases, and some neoplasms. Today, microbiome research is not only essential for understanding health and disease mechanisms but also forms the foundation for innovative future medical applications.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"307-331"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147513874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Energy Metabolic Regulatory Materials Promote Wound Healing in Senescent Environment.","authors":"Xuetong Wang, Tingbin Zhang, Huan Zhou, Lei Yang","doi":"10.1007/978-3-032-17771-1_1","DOIUrl":"10.1007/978-3-032-17771-1_1","url":null,"abstract":"<p><p>Chronic wounds, pathological states failing to heal promptly, are especially prevalent among the elderly. This impaired healing in the senescent tissue is predominately attributed to the accumulation of senescent cells and a concomitant decline in energy metabolism, ultimately leading to functional impairment. Existing clinical practices-including debridement, hyperbaric oxygen, antibiotics, and wound dressings-cannot fundamentally resolve this cellular decline. In this context, advanced biomaterials designed to enhance cellular energy metabolism emerge as a viable strategy. This chapter details strategies by which biomaterials enhance skin wound healing in aging environments by modulating energy metabolism. It explains that delayed healing primarily stems from age-associated metabolic and mitochondrial dysregulation, which compromises cellular repair functions. Furthermore, it reviews advanced biomaterial-based approaches that promote healing by delivering metabolites, restoring mitochondrial function, and indirectly modulating stem cells. By targeting energy metabolism to reverse the low-energy state of aged skin, these approaches fundamentally address cellular functional decline and actively foster tissue regeneration. Therefore, this chapter outlines design principles for energy metabolism-modulating biomaterials to aid wound healing in aged skin and highlights recent advances in this field.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"63 ","pages":"1-45"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147284866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial Evolution and Systematics: Archaea and Bacteria.","authors":"Hilal Ay","doi":"10.1007/978-3-032-11438-9_1","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_1","url":null,"abstract":"<p><p>The origin of life on Earth is a profound biological question, with Bacteria and Archaea-the two principal prokaryotic lineages-central to the inquiry. Together, they represent microbial diversity and offer insights into Earth's earliest biosphere and evolutionary history. Microorganisms are of significant relevance to humanity, not only as disease agents for some infections but also due to their indispensable contributions to ecosystem functioning, primarily because of their involvement in biogeochemical cycling in various habitats. They influence soil fertility, plant growth, and the overall stability of biological communities across different habitats by mediating the turnover of energy and matter through processes such as decomposition, nutrient cycling, and regulating atmospheric gases. The fields of microbial evolution and systematics are mainly concerned with elucidating the origins, diversification, and classification of these two domains of life. These disciplines are fundamental for comprehending the extensive diversity of life on Earth and the evolutionary mechanisms that have shaped it. Notably, horizontal gene transfer, recombination, mutation, and selection are key evolutionary mechanisms driving genetic innovation and ecological differentiation in microbial populations, influencing phylogeny, function, and ecosystem dynamics. Advances in genomics and bioinformatics have transformed microbial systematics by enhancing polyphasic taxonomy through the integration of phenotypic and phylogenetic data, and have also provided valuable tools to gain deep insight into microbial evolution. This chapter examines the evolutionary history of microorganisms in the context of Bacteria and Archaea, the mechanisms underlying their evolution, the modern methodologies employed in microbial systematics, and the broader implications of these studies for science and society.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"1-45"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147514370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biotechnological Applications of Archaea.","authors":"Nalan Tavşanlı, Ahmet Arıhan Erözden, Muzaffer Arıkan, Mahmut Çalışkan","doi":"10.1007/978-3-032-11438-9_6","DOIUrl":"https://doi.org/10.1007/978-3-032-11438-9_6","url":null,"abstract":"<p><p>Archaea are the \"silent and unseen majority of life\" with an extraordinary capacity to live in some of the most unfavorable habitats in nature, and continue to exist in regions with extreme features that are inhospitable to most other living organisms. They are prokaryotic and frequently found in environments with high pH, salinity, and temperatures. Asgard, Euryarchaeota, TACK, and DPANN are the four main superphyla that make up the Archaea, one of the three domains of life on Earth. Extremophiles, the first Archaea found, are classified into four major physiological types. These are halophiles, thermophiles, alkaliphiles, and acidophiles. The Archaea domain is the subject of extensive research, particularly for potential biotechnological applications. Archaea play a crucial role in environmental sustainability and human health, particularly through their enzymes, metabolites, and biochemical processes. These are some core characteristics of Archaea enabling biotechnological usage. This chapter aims to provide an overview of the various roles that Archaea have in biotechnological usage, both current and potential. Their classification is based on the industry to which the application is targeted, which includes industrial enzyme and catalysis, energy production, and medical and pharmaceutical applications.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"62 ","pages":"191-216"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147514430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advanced Strategies in the Repair of Alveolar Cleft Defects: Biological Approaches, Biomaterials, and Future Perspectives.","authors":"Muhammad Ruslin, Carolina Stevanie, Andi Tajrin","doi":"10.1007/978-3-032-17771-1_7","DOIUrl":"10.1007/978-3-032-17771-1_7","url":null,"abstract":"<p><p>The repair of alveolar cleft defects remains a formidable challenge in craniofacial surgery, with implications for dental arch continuity, tooth eruption, speech, and facial aesthetics. Traditional bone grafting methods (especially iliac crest autografts) have remained the gold standard, yet donor-site morbidity, graft resorption, and limitations in large defects drive the search for more advanced strategies. In recent years, developments in biomaterials, stem cell-based tissue engineering, and computer-aided surgery have opened new conceptual and practical pathways for alveolar cleft repair. This chapter reviews the embryology and pathophysiology of alveolar clefts, the structural and functional sequelae, and conventional surgical approaches. It then delves into advances in scaffold design, growth factor delivery, mesenchymal stem cell therapies, and 3D bioprinting strategies, highlighting preclinical and early clinical findings. Additionally, the role of CBCT, CAD/CAM, and custom surgical guides is examined in improving graft placement, reducing surgical error, and optimizing outcomes. Clinical successes and persistent challenges are analyzed, including graft integration, long-term stability, tooth eruption, and ethical/regulatory issues. We conclude by identifying key research gaps and proposing future directions-such as scaffold-free regeneration, AI-driven planning, and patient-specific regenerative protocols-that may transform alveolar cleft management in the coming decade.</p>","PeriodicalId":20880,"journal":{"name":"Progress in molecular and subcellular biology","volume":"63 ","pages":"209-235"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147284834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}