Loop-mediated isothermal amplification (LAMP) is widely used when rapid nucleic acid detection with minimal instrumentation is required. This review focuses on methylation-sensitive LAMP (MS-LAMP), a narrower and still underdeveloped extension in which methylation status is converted into an amplification outcome. We concentrate on microbiology-relevant applications and discuss the two principal gating routes currently used: bisulfite conversion followed by methylation-discriminating primer design, and methylation-sensitive restriction enzyme digestion before amplification. Rather than reviewing LAMP broadly, we examine how methylation gating reshapes assay design, readout selection, upstream quality control, and result interpretation. We also distinguish direct MS-LAMP evidence from the larger supporting literature on microbial methylomes and general LAMP engineering. Current evidence suggests that the main translational bottlenecks lie upstream of amplification, particularly in template damage during bisulfite treatment, digestion specificity, control design, and performance in complex clinical matrices. We conclude that MS-LAMP remains promising but methodologically immature for routine microbiology, and that progress will depend on robust locus selection, process controls, predefined thresholds, and validation across clinically relevant specimen types.
Biofilm formation is a key microbial survival mechanism that enables bacterial persistence and recurrence of urinary tract infections (UTIs), especially in patients with catheters or structural abnormalities. These complex microbial communities hinder antibiotic efficacy and facilitate the development of antibiotic resistance. Recent advances in microbiology and materials science have led to the emergence of diverse therapeutic approaches targeting biofilms. This review highlights current and investigational strategies for biofilm disruption, including the inhibition of quorum sensing, enzymatic or chemical degradation of extracellular polymeric substances, antimicrobial peptides, nanoparticle-based systems, and microbiota modulation. Understanding these evolving modalities may guide future individualized treatments for recurrent UTIs.
Millet fermentation has gained significant attention due to its numerous health benefits, owing to its higher dietary fiber and gluten-free properties, making it suitable for celiacs, individuals with diabetes, and higher heart risk due to its low glycemic index and low-calorie content. This review critically highlights the current knowledge available about the potential smart technologies in millet fermentation, offering insights into food safety and quality concerns. A thorough literature search was conducted based on recent studies demonstrating the smart fermentation technologies in millet. The findings of this review suggested that the application of smart technologies in millet fermentation can improve precision and efficiency of fermentation process optimization, yield enhancement, and functional attributes. However, only limited applications of smart technologies were employed for millet fermentation, and more advanced and optimized technologies are yet to be explored and implemented for better outcomes. The current millet fermentation studies are mostly of concern towards the beneficial microorganisms, compromising the potential threats of pathogenic organisms if fermentation conditions are not maintained. Integrating advanced machine learning, modeling, and hazard analysis during the fermentation process would lead to attaining safety against contaminants, microbial contamination, toxins, and hazards in millet-based fermented products with assured quality.
Cellular agriculture (CA), an emerging and sustainable agricultural paradigm, offers a promising solution to global challenges in food security and environmental sustainability. However, the large-scale manufacturing of CA is hindered by its dependence on serum-based culture media, which are costly and compositionally variable and raise biosafety and animal welfare concerns. Addressing this bottleneck requires the development of affordable, reliable, and ethically compliant serum-free media (SFM). This perspective elucidates the functional roles of serum components, summarizes recent advances in serum substitutes, and highlights microorganism-derived substitutes as particularly promising because of their low cost, compositional stability, and scalability. Furthermore, we outline the evolution of SFM formulation from empirical and design-of-experiment-based optimization to multiomics-driven formulation and artificial intelligence (AI)-assisted design. Overall, this review provides a focused framework for understanding current challenges, design strategies, and future directions of SFM development for CA.
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. cubense (Foc) Tropical race 4 (TR4) is currently devastating Cavendish banana production worldwide. The availability of accurate and rapid field-deployable detection tools is vital for effective disease prevention and containment practices, as no effective treatment is currently available. Design of reliable molecular detection tools, however, is challenged by genetic similarity between non-pathogenic and target Foc strains that are present in symptomatic plant material. The high genetic diversity present among Foc isolates further complicates the identification of unique genomic regions suitable for diagnosis. Current molecular assays are also still mostly confined to laboratory settings and rely on expensive equipment that needs skilled operators to perform. In the present study, a simple loop-mediated isothermal amplification (LAMP) detection assay was developed for direct in-field detection. A comprehensive database of Foc genomes including 148 TR4 genomes and 146 non-target genomes was used, considering the wide diversity within Foc. These genomic sequences were exploited in a comparative genomics in silico pipeline using the KEC method (K-mer elimination by cross-reference), combined with filtering steps using BLASTn, and Illumina read alignments. The specificity of the LAMP primers was validated using a diverse collection of 161 isolates, which included Foc-TR4 isolates, Foc VCGs, F. oxysporum spp. endophytes, other Fusarium spp., and genera which are commonly isolated from banana vascular tissue. The limit of detection reached 102 copies µL-1 of plasmid DNA, and the target pathogen was successfully identified both from artificially inoculated and naturally infested material in contrasted environments, indicating the LAMP assay to be a robust and reliable tool fully suitable for field diagnosis.
Syphilis is a leading cause of adverse pregnancy outcomes, excessively affecting sub-Saharan Africa. Early diagnosis and treatment are crucial to prevent mother-to-child transmission. The aims of the present study were to assess prevalence and epidemiological and clinical correlates of active syphilis diagnosed using serological [treponemal and non-treponemal (lipoidal)] assays and the research-use-only (RUO) Aptima Treponema pallidum assay [Hologic; transcription-mediated amplification (TMA) assay] among pregnant women attending four antenatal care facilities in Nchelenge, Zambia in 2023. Syphilis serology was performed using rapid diagnostic test [RDT; Core tests® ONE STEP Syphilis Test Kit (Core Technology, Atlanta, USA)]; positive samples were further evaluated by rapid plasma reagin [RPR; RPR Carbon Antigen Reagent (Eurocarb Products Ltd., Bristol, United Kingdom)] test. Active syphilis was defined as a positive RDT plus a positive RPR test, or a positive RUO Aptima T. pallidum assay. T. pallidum and other non-viral STIs (Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis) were detected in clinician-collected vaginal swab samples using Aptima assays on the Panther system (Hologic). HIV testing was performed with the Determine HIV Test Kit, and bacterial vaginosis (BV) was diagnosed using Nugent's score. Active syphilis correlates were identified using univariable and multivariable logistic regression. In total, 996 pregnant women were included in the analysis, of whom 136 women (13.7%) had an active syphilis infection. Of these women with active syphilis, 117 (86.0%) were positive in serology only, 15 (11.0%) in serology plus RUO Aptima T. pallidum assay, and four (2.9%) in RUO Aptima T. pallidum assay only. Rates of other current STIs and reproductive tract infections included: BV (23.3%), T. vaginalis (22.7%), M. genitalium (12.7%), HIV (8.7%), N. gonorrhoeae (8.4%), and C. trachomatis (7.4%). Secundigravidity, history of stillbirth, current concomitant M. genitalium, N. gonorrhoeae, T. vaginalis, and HIV infections were significant risk factors of active syphilis. Advanced gestational age (from 28 to 39 weeks) at enrolment was associated with significantly lower risk of syphilis positivity. A remarkably high burden of syphilis and high co-infection rates with HIV and other non-viral STIs in pregnant women in Zambia underscore the urgent need for integrating syphilis and HIV universal screening programs, as well as to consider concurrent testing for selected other non-viral STIs. Where feasible due to the increased cost, supplementing serological screening with a highly sensitive and specific molecular test such as the RUO Aptima T. pallidum assay for suspected early syphilis can ensure timely detection of both seroconverted and seronegative early syphilis cases, early treatment and effective prevention of mother-to-child transmission.
Current guidelines based on expert opinions recommend a minimum of 4-6 weeks of antibiotic treatment for paediatric Salmonella osteoarticular infections. In this study, we aim to validate guidelines and investigate the duration of antibiotic treatment. PubMed, Medline, Embase, Scopus, and Google Scholar were searched for cases according to the PRISMA guidelines. We included all paediatric cases from January 1990 to December 2025 with confirmed Salmonella osteoarticular infection. Outcome was reported in 173 (81%) of 214 children; 117 (68%) previously healthy children fully recovered after a median antibiotic treatment duration of 6.0 weeks, and 32 (18%) children with comorbidities including sickle cell disease fully recovered after a median duration of 8.0 weeks. For all children, approximately half of the treatment duration was administered intravenously. Multivariable logistic regression analysis demonstrated no independent association between antibiotic treatment duration and outcome. The majority of children fully recovered after an antibiotic treatment duration within the current guidelines of minimum four weeks in case of joint infection only and six weeks in case of bone infection. The variation in antibiotic treatment durations was substantial. Individualized treatment durations within the recommended timeframe seem reasonable based on the clinical and paraclinical response.
Naganishia (N.) uzbekistanensis is a rare basidiomycetous yeast within the family Filobasidiaceae, widely distributed in environmental niches, with very limited clinical data available. Its clinical and microbiological features remain poorly understood, posing diagnostic challenges in clinical microbiology laboratories. We describe a pulmonary infection caused by N. uzbekistanensis strain CY11558 and present an expanded laboratory investigation of this previously reported clinical strain. The strain was analyzed using a comprehensive laboratory workflow that included conventional culture, light microscopy, scanning electron microscopy (SEM), and molecular identification based on rDNA sequencing. Phylogenetic analysis was conducted to assess the genetic relationship with reference strains. Antifungal susceptibility testing and in vitro Titan cell induction assays were also performed. Conventional MALDI-TOF MS failed to identify the strain, while rDNA sequencing confirmed N. uzbekistanensis. Cryptococcal antigen testing yielded a weakly positive result with the pure culture supernatant, while the patient's serum remained negative. The strain showed markedly elevated MICs for echinocandins, flucytosine, and fluconazole, whereas MICs for voriconazole, itraconazole, and amphotericin B were comparatively low. Microscopic examination revealed round yeast cells without pseudohyphae. SEM showed globular cells enveloped by a fibrillar network. Titan cell formation was not observed. Phylogenetic analysis demonstrated intraspecies variability without geographic association. This study provides comprehensive phenotypic, including antifungal susceptibility, and molecular characterization of N. uzbekistanensis, emphasizing the need for molecular tools in identifying uncommon yeasts. The findings expand current understanding of its morphological and resistance traits and highlight potential diagnostic challenges in clinical laboratories.
Silibinin is the primary bioactive flavonolignan in silymarin derived from Silybum marianum and has attracted significant scientific interest because of its diverse pharmacological properties. This review summarizes current evidence on its molecular mechanisms, pharmacological activities, and preclinical and clinical applications. Experimental data indicate that silibinin exerts potent antioxidant, anti-inflammatory, antifibrotic, and anticancer effects by modulating multiple signaling pathways involved in oxidative stress, cytokine production, apoptosis, and cell proliferation through the redox-onco axis. Reactive oxygen and nitrogen species contribute to tumor initiation and progression by activating key signaling pathways, including the NF-κB, PI3K/Akt/mTOR, and HIF-1α pathways. Silibinin has dual, context-dependent effects: it scavenges free radicals and activates the Nrf2-Keap1 pathway to protect normal cells while selectively disrupting redox homeostasis in cancer cells, thereby leads to apoptosis and autophagy. Moreover, it inhibits cell proliferation through inducing G1/S or G2/M cell cycle arrest, suppresses angiogenesis by downregulating vascular endothelial growth factor, and reduces metastasis by inhibiting matrix metalloproteinases and epithelial-mesenchymal transition. In addition to these effects, silibinin enhances DNA repair and modulates epigenetic regulators to counteract oxidative damage. Despite such promising preclinical and clinical findings, its therapeutic ability is currently limited by poor aqueous solubility and low bioavailability. To overcome these pharmacokinetic limitations, researchers have developed novel drug delivery systems, such as nanoformulations and phospholipid complexes. Ultimately, silibinin has emerged as a multifunctional natural compound with significant therapeutic benefits. However, further mechanistic investigations and well-designed clinical trials are required to validate its efficacy and optimize dosage.
Acquired immunodeficiency syndrome (AIDS) is one of the most dangerous diseases threatening global public health. Antiretroviral therapy (ART) is currently the primary treatment for people living with HIV (PLWH). However, some patients are classified as immunological non-responders (INRs), defined by the failure to achieve adequate CD4+ T cells reconstitution despite continuous viral suppression, and are associated with inferior clinical outcomes. This behavior may be linked to the ongoing dysfunction of the intestinal microenvironment. Although PLWH exhibit similar clinical changes such as intestinal mucosal injury, barrier failure, and microbial community problems, intestinal microenvironment abnormalities in INRs are more severe. The specific manifestations include persistently low levels of intestinal CD4+ T cells with limited reconstitution, along with a significant reduction in the proportion of Th17 cells, leading to severe impairment of mucosal anti-infective capacity and immune regulatory function. Additionally, elevated levels of pro-inflammatory mediators drive chronic inflammation, thereby exacerbating tissue damage. Furthermore, microbial dysbiosis is more pronounced, characterized by a marked decrease in beneficial symbiotic bacteria and an expansion of opportunistic pathogens. In contrast, immunological responders showed some degree of recovery in these indicators. These pathological features are not only associated with a higher risk of disease progression and complications in INRs but also provide a theoretical basis for developing adjuvant treatment strategies targeting intestinal immune reconstitution. In addition, we summarize the current mainstream definitions of INRs and propose a more robust definition. This review systematically elaborates the pathogenic mechanisms and potential intervention strategies underlying intestinal microenvironment abnormalities in INRs and holds important clinical value for improving the long-term prognosis of patients and advancing individualized treatment.
Scabies remains a major cause of morbidity among Bangladeshi children, particularly in overcrowded and resource-limited settings. This perspective synthesizes current evidence to contextualize the surge of pediatric scabies outbreaks reported across Bangladesh in 2025. This perspective aimed to map outbreak hotspots, identify key risk determinants, and highlight health system gaps in surveillance and diagnosis, and therapeutic management of scabies. Evidence was compiled from published literature, national health data, WHO reports, media alerts, interviews with 50 registered dermatologists, and ArcGIS-based visualization of affected regions. Outbreaks were widespread across urban slums, religious school (Madrasa), Rohingya refugee camps, university dormitories, flood-affected districts, rural communities and multiple districts including Cumilla, Barisal, Noakhali, Rajshahi, Sylhet, Khulna, Mymensingh, and Cox's Bazar driven by poverty, overcrowding, poor sanitation, seasonal humidity, and limited access to dermatologic care. Treatment practices reported by surveyed physicians revealed that 5% permethrin cream remains the first-line therapy, while oral ivermectin is increasingly used for severe, recurrent outbreaks, although availability and affordability remain inconsistent across districts. Reinfection rates in institutional settings and the absence of national surveillance systems further complicate control efforts. This perspective emphasizes the urgent need for integrated strategies, including strengthened surveillance, improved treatment access, community-based hygiene interventions, and alignment with WHO's NTD roadmap. Strengthening these components is essential to reduce pediatric morbidity, prevent complications, and enhance Bangladesh's progress toward effective scabies control.
Intracranial aneurysm (IA) prevalence in the general population can be as high as 3%. Most IAs are asymptomatic and diagnosed incidentally. However, IAs can cause subarachnoid hemorrhage (SAH), which is responsible for high mortality and morbidity. No effective medical therapy is currently available to control the IA and reduce the SAH risk. Understanding IA pathophysiology to identify potential targets is, therefore, an essential clinical objective. IAs typically form at arterial bifurcations and are characterized by macrophage infiltration. Macrophages are innate immune cells that present antigens to adaptive immune cells and promote inflammation. The potential role of macrophages in IA was demonstrated when inhibiting the macrophage recruitment contained aneurysm formation or growth. Recent advances in spatial transcriptomics enable the study of infiltrating macrophages within the aneurysmal lesion and the identification of pathogenic changes that were previously challenging to probe. While sample availability may limit the use of spatial transcriptomics, judicious use of IA animal models will enable translational research to address unmet clinical needs. With spatial insights and refined animal models, researchers can identify key characteristics of infiltrating macrophages, including their ontogeny, transcriptomic profiles, and interactions with other cell subsets. This review article summarizes the current understanding of infiltrating macrophages in IAs and introduces available animal models of IA and spatial transcriptomics approaches for studying macrophage infiltration.
MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) technology has become an effective tool in clinical mycology laboratories in recent years for the identification of pathogenic filamentous fungi. A total of 527 clinical specimens, comprising samples from both superficial and deep mycoses, were included in this study. Filamentous fungal samples isolated from various clinical specimens and identified using conventional methods between 2017 and 2018 at the Medical Microbiology Mycology Laboratory of Istanbul University-Cerrahpaşa Faculty of Medicine Hospital were analyzed using MALDI Biotyper Bruker Daltonik GmbH Revision 4 and the Filamentous Fungi database v3.0. In the identification of mold samples, the highest scoring identification values ​​were determined with the liquid cultivation and extraction method recommended by MALDI-TOF MS for filamentous fungi. A total of 46 different filament fungi species, including 6 dermatophytes and 40 non-dermatophyte filament fungi species, were identified from the clinical samples in the study. Of the total of 527 clinical samples, 27% (n = 142) were identified as having high reliability in the range of 1.8 to 3, and 20% (n = 103) as having low reliability in the range of 1.6 to 1.79. The total rate of identified filament fungi was successfully determined as 47% (n = 245). In the practical experience of our medical mycology laboratory, we evaluated the current uses of MALDI-TOF MS and their practical application in daily routine. In the identification of mold species obtained from clinical samples by MALDI-TOF, it is important to meticulously prepare sample preparation protocols, use an identification strategy suitable for routine diagnosis, and continuously update libraries using advanced databases.
In the context of gamete donation, cytomegalovirus (CMV) serological screening was originally implemented to mitigate concerns about viral transmission, particularly following the HIV epidemic. Although emerging evidence questions the reliability of serological markers in accurately reflecting the presence of the virus in genital secretions, current North American practices still heavily rely on CMV serological testing to identify sperm donors at risk of transmitting CMV during fertility treatments. This review explores the complexities of CMV transmission in assisted reproductive technologies (ART), underscoring the unpredictable nature of viral shedding in semen and the inherent limitations of relying solely on serostatus for risk assessment. Additionally, the available data suggest that the risk of congenital CMV (cCMV) following ART appears low, although significant gaps in the literature highlight the need for more comprehensive studies to better evaluate transmission risks. Finally, this review advocates for the revision of CMV screening societies' guidelines, emphasizing the need for broader, evidence-based preventive strategies. Preventing CMV risk in fertility treatments may include more significant action such as patient education on simple hygiene measures to prevent infection during pregnancy-instead of current, potentially unnecessary measures such as CMV serostatus matching.
One of the major challenges for malaria elimination is combating the highly efficient spread of the disease. Despite progress in understanding the development of malaria transmission stages, there remain many unanswered questions about how gametocytes transition from being immature to infectious. In Plasmodium falciparum, immature gametocytes are rigid and sequester outside of circulation in the extravascular space of the bone marrow, while deformable, mature stages are found in circulation and transmitted to mosquitoes. It is currently unclear whether deformable gametocytes are immediately infectious to mosquitoes, or whether they undergo activation upon release into circulation. We used a combination of phenotypic assays and transcriptional analysis to define the transition from immature non-infectious to mature infectious gametocyte. Specifically, we associated gene expression with distinct phenotypic traits: gametocyte deformability assessed by microsphere filtration, and gametocyte infectivity assessed by exflagellation and mosquito feeding assays. Our data revealed major transcriptional differences between input and deformable (i.e., filtered) gametocytes, but high similarity between deformable and infectious gametocytes. In combination with exflagellation and transmission results upon mosquito feeding assays, this suggests that deformable gametocytes are immediately infectious upon release from the bone marrow. The transcriptional analysis revealed a comprehensive set of infectivity markers that can be utilized to track gametocytes during their development and serve as diagnostic tools to map the human infectious reservoir. Malaria spreads when mosquitoes ingest specialized malaria life stages, called gametocytes, from infected people. For the deadliest malaria parasites, Plasmodium falciparum, gametocytes undergo a long maturation process. Young gametocytes of this parasite are stiff and hidden in the bone marrow. Following maturation, the gametocytes become more flexible and are released into the bloodstream. It remained unclear whether these flexible gametocytes are immediately infectious to mosquitoes or need further maturation. The current study examined changes in the gametocyte, from stiff to deformable and from non-infectious to infectious, in relation to gene activity. The results show that once gametocytes become flexible and enter the bloodstream, they are already infectious. The study also identified genetic markers linked to infectivity, which could help track malaria transmission and improve tools to identify people who can spread the disease.
Kawasaki disease (KD) is an acute, immune-mediated medium-vessel vasculitis and the leading cause of acquired heart disease in children, yet its underlying etiology remains only partially defined. Emerging evidence implicates the gut microbiota as a key modulator of KD susceptibility, immune dysregulation, and therapeutic response. This narrative review aims to synthesise current insights linking gut microbial dysbiosis and microbial metabolites to the pathogenesis, clinical expression, and treatment of KD, and to explore microbiome-informed strategies with diagnostic and therapeutic potential. We conducted a comprehensive search of PubMed, Embase, Web of Science, and Google Scholar from database inception to April 2025 for English-language studies on Kawasaki disease and the gut microbiota, including terms related to microbiome, microbial dysbiosis, metabolites, pathogenesis, immunity, inflammation, and therapy. Reference lists of relevant articles and key reviews were also screened. Children with acute KD exhibit characteristic alterations in gut microbial composition, including an overrepresentation of Streptococcus species, depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium, Ruminococcus, and Roseburia, and a significant reduction in fecal butyrate. These changes have been associated with impaired intestinal barrier integrity, heightened NLRP3 inflammasome activation, and dysregulated cytokine signalling, contributing to systemic inflammation and vascular injury. Additional factors, such as antibiotic exposure and concurrent respiratory or oropharyngeal infections, can intensify dysbiosis and have been linked to resistance to intravenous immunoglobulin (IVIG) and an increased risk of coronary artery aneurysms. Conclusions: Gut microbial imbalance and metabolite disruption are likely associated with KD, potentially through interaction with host genetics and immune pathways. Microbiome-targeted approaches, including probiotics, dietary modulation, and metabolite-based therapies, hold promise for improving diagnostic precision, predicting treatment response, and guiding the development of targeted interventions in KD.
This study aims to explore the performance of metagenomic next generation sequencing (mNGS) in the diagnosis of non-neutropenic invasive pulmonary aspergillosis (IPA) and its clinical application value. This multi-center study enrolled 293 suspected IPA patients who conducted mNGS from October 2020 to February 2024. These cases were classified into IPA group and non-IPA group according to IPA diagnostic criteria. We analyzed the diagnostic value of mNGS by comparing with sputum culture, BALF culture, serum and BALF GM test. A total of 118 IPA patients (4 proven/113 probable/1 possible diagnosis) were included in our study. The most common Aspergillus species was A. fumigatus (63.4%), followed by A. flavus (23.2%), A. oryzae (7.1%), A. niger (3.6%) and A. terreus (2.7%). The sensitivity of bronchoalveolar lavage fluid (BALF) mNGS was significantly higher than BALF culture (81.9% vs. 27.0%, p<0.001) and BALF galactomannan (GM) (81.9% vs. 55.8% (GM≥1.0 cutoff value), p<0.001). The specificity of BALF mNGS was 92.2%, which was similar with BALF culture (98.5%) and BALF GM (94.7%). The combination of BALF mNGS and GM could increase the sensitivity to 88.7%, and had great negative predictive value (NPV, 92.3%). The sensitivity of blood mNGS was significantly higher than serum GM (58.8% vs. 16.7%, p<0.001). And the sensitivity of sputum mNGS was 66.7%, which was significantly higher than sputum culture (30.0%, p=0.025). mNGS demonstrated significant diagnostic value for IPA, exhibiting significantly higher sensitivity compared to current conventional microbiological tests while maintaining equivalent specificity. The combination of BALF mNGS with GM performed great sensitivity and negative predictive value. BALF specimens seemed to be superior to blood and sputum samples. However, for patients unable to undergo bronchoscopy, sputum and blood mNGS were still superior to other methods.
Symbiotic nitrogen fixation (SNF) by legumes is essential for sustainable agriculture, providing plant-available nitrogen while reducing reliance on synthetic fertilizers. The establishment of legume-rhizobium symbiosis requires tightly regulated host signaling to coordinate rhizobia infection, nodule development, and nitrogen fixation, while preventing excessive colonization or immune activation. Accumulating evidence indicates that ubiquitination, mediated by E1, E2, E3 ubiquitin ligases and deubiquitinating enzymes, plays a central role in controlling multiple stages of this process. In this review, we summarize current knowledge on ubiquitination-mediated regulation of symbiotic nitrogen fixation, with a focus on early symbiotic signaling and nodule development. We highlight key E3 ligases that modulate Nod factor receptor homeostasis, receptor-associated kinases, transcription factors, and infection thread growth, and discuss how ubiquitination interfaces with nutrient and stress signaling pathways. Finally, we outline key knowledge gaps and discuss the potential of manipulating ubiquitination pathways to improve nodulation efficiency and nitrogen use efficiency in crops.
Escherichia coli has been widely engineered as a microbial chassis for the biosynthesis of a broad spectrum of products ranging from basic building blocks and biocommodities to high-value fine chemicals and drugs. However, most current bioprocesses still rely on conventional feedstocks such as corn-derived glucose and sugarcane-derived sucrose, which are also demanded by established food and industrial supply chains. Consequently, allocating these sugars to the production of biocommodities, which are required in large quantities and at low cost, may exacerbate concerns about food security and undermine the long-term sustainability of large-scale biomanufacturing relative to low-cost petrochemical routes, particularly for bulk chemicals. Lignocellulosic biomass, derived from agricultural residues and urban waste, presents a low-cost, renewable, and abundant alternative source of fermentable sugars. Composed of an intricate matrix of cellulose, hemicellulose, and lignin, lignocellulose exhibits a high degree of structural recalcitrance. To access its fermentable components, biomass typically needs physicochemical pretreatment and enzymatic saccharification using commercial cellulases. Unfortunately, these enzymes are expensive, and their optimal catalytic properties are typically achieved under conditions incompatible with those required by conventional E. coli production strains, thereby complicating the integration of saccharification and fermentation processes. To overcome this barrier, significant efforts have been made to engineer recombinant cellulolytic E. coli strains capable of degrading cellulose. Strategies explored include intracellular expression of cellulases followed by induced lysis, enzyme secretion via signal peptides, and surface display of cellulolytic enzymes, among others. Key advances toward achieving saccharolytic E. coli have been achieved. Proof-of-concept studies have demonstrated simultaneous saccharification and fermentation using pretreated lignocellulosic biomass, and high-throughput platforms for evolving cellulolytic enzymes have been established. Despite substantial progress, knowledge in this field remains fragmented across diverse studies. This review consolidates key advancements in the development of cellulolytic E. coli strains, emphasizing the molecular, metabolic, and physiological engineering strategies employed. It also highlights key challenges and future directions for integrating lignocellulose utilization into industrial E. coli-based bioprocesses.
During a survey of helicosporous hyphomycetes in tropical regions of China, four fungal strains were isolated from decaying wood in freshwater habitats of Hainan Province. Multi-locus phylogenetic analyses (LSU, ITS, tef1-α, and rpb2), coupled with detailed morphological examinations, support the recognition of two new species, Neohelicomyces baochengensis and N. xiangshuiensis. Comprehensive morphological descriptions, illustrations, taxonomic notes, and phylogenetic evidence are provided to clarify their systematic placement. These findings broaden the current understanding of Neohelicomyces diversity and provide further records of the genus from tropical freshwater habitats in Hainan Province.