Biotechnology Reports最新文献

{"title":"The interplay of serum cations, insulin resistance, and atherogenic indices in predicting depression in hypothyroid patients","authors":"Sahira Qasim Al-Baldawi ,&nbsp;Hussein Kadhem Al-Hakeim ,&nbsp;Habib Hamam ,&nbsp;Ikram Khémiri","doi":"10.1016/j.btre.2025.e00932","DOIUrl":"10.1016/j.btre.2025.e00932","url":null,"abstract":"<div><h3>Background:</h3><div>A significant proportion of people with hypothyroidism (HT) is linked to affective disorders, including depression. The pathophysiology and factors affecting or predicating depression in HT patients is still to be elucidated. The current study intends to investigate serum levels of cations, insulin resistance parameters, trace elements and atherogenic indices, in HT+Dep, HT, and healthy control groups.</div></div><div><h3>Methods:</h3><div>We measured the biomarkers in the blood of sixty HT+Dep patients, sixty HT patients, and healthy controls who participated in the study. Selenium was measured using flameless atomic absorption spectrophotometry. While insulin level was measured using the ELISA technique.</div></div><div><h3>Results:</h3><div>We observed significant insulin resistance (IR) and dyslipidemia in HT patients, which were more pronounced in HT+Dep. Moreover, HT+Dep patients exhibited alterations in the blood concentrations of cations and trace elements. Artificial neural network analysis demonstrated that the atherogenic index of plasma (AIP) is the most precise predictor of depression in HT patients, with a success rate of 100%. This was followed by the distance from Castelli’s risk index-I (CRI-I) (24.7%), ionized calcium (23.1%), the IR index (HOMA2IR) (22.4%), and the insulin sensitivity index (HOMA2S%) (21.8%). Selenium, conversely, was the most reliable biomarker for differentiating the HT group from the control group.</div></div><div><h3>Conclusion:</h3><div>Depression in HT patients is associated with alteration in the serum levels of cations, atherogenic indices, trace elements, and IR. AIP is the best predictor for depression in HT patients. It is essential to correct the amounts of blood biomarkers of HT patients to mitigate the severity of depression.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00932"},"PeriodicalIF":0.0,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473730","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":"Basic assessment of microbial dynamics in large- and small-scale biofilters","authors":"Andreas Otto Wagner ,&nbsp;Julia Wurm ,&nbsp;Mathias Wunderer ,&nbsp;Julia Zöhrer ,&nbsp;Andja Mullaymeri ,&nbsp;Eva-Maria Weinseisen ,&nbsp;Eva Maria Prem","doi":"10.1016/j.btre.2025.e00936","DOIUrl":"10.1016/j.btre.2025.e00936","url":null,"abstract":"<div><div>Treating exhaust gas from biogas plants is commonly done using biofilters composed of different filter materials. Immobilized on these filter materials microbes can convert less desirable exhaust gas components into more wanted ones. The evaluation of the performance of those filters based on microbial data is, however, difficult due to a lack in data regarding microbial colonisation of these filter materials. Thus, in the present study microbial abundance and microbial community composition in large- and small-scale biofilters was evaluated using both, cultivation dependent and independent approaches. Large-scale biofilters showed a similar total abundance of bacteria irrespective of the filter material and the water content of the biofilter. In contrast, fungal and yeast abundance was impacted by both, filter material (bark mulch or coconut fibre) and water content. In small scale biofilters (composed of bark mulch) the water content impacted microbial abundance. While a water content of 90% led to a similar development of bacterial and fungal/yeast abundance, 70% water content caused an asynchronous increase in abundance. Analysis of small-scale biofilters revealed an acidotrophic bacterial community including potential methanotrophs.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00936"},"PeriodicalIF":0.0,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473797","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":"Enhanced CO2 sequestration and paramylon production in acid-tolerant Euglena gracilis: Growth optimization and metabolic response under varying CO2 concentrations","authors":"Tia Erfianti ,&nbsp;Brilian Ryan Sadewo ,&nbsp;Nugroho Dewayanto ,&nbsp;Adib Fakhruddin Yusuf ,&nbsp;Dedy Kurnianto ,&nbsp;Deviko Mardyansah ,&nbsp;Ikhnu Prawestri Wardani ,&nbsp;Budi Setiadi Daryono ,&nbsp;Eko Agus Suyono ,&nbsp;Marcos ,&nbsp;Arief Budiman","doi":"10.1016/j.btre.2025.e00935","DOIUrl":"10.1016/j.btre.2025.e00935","url":null,"abstract":"<div><div><em>Euglena gracilis</em> is a microalgae suited for acidic environments and efficient CO₂ absorption, making it a strong candidate for biological carbon fixation. This study examined its growth, biomass, lipid and paramylon production, and metabolic responses under varying CO₂ levels (0.04 %, 5 %, 15 %, 30 %). Optimal results were observed at 5 % CO₂, with peak biomass (0.407 ± 0.099 g/L), lipid (0.189 ± 0.025 g/L), and paramylon (0.0159 ± 0.0034 g/L) on day 6. SEM showed oval to ellipsoid paramylon granules (0.5–2.5 µm), while GC–MS revealed isophytol acetate (31.44 %) as the major fatty acid. Upregulation of <em>RubisCO</em> and <em>EgGSL1</em> genes indicated enhanced carbon fixation and paramylon synthesis. A 12 L pilot-scale culture confirmed high CO₂ uptake (0.429 g·L⁻¹·day⁻¹). These findings support <em>E. gracilis</em> as a promising platform for CO₂ sequestration, bioresource production, and paramylon-based bioproducts, with further research needed for industrial scalability.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00935"},"PeriodicalIF":0.0,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145525441","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":"Enhancing enzyme activity of heterologously expressed Chit42 in Nicotiana benthamiana for chitin degradation","authors":"Naser Mirhosseini Motlagh ,&nbsp;Mostafa Motallebi ,&nbsp;Zahra Moghaddassi Jahromi ,&nbsp;Lukhanyo Mekuto","doi":"10.1016/j.btre.2025.e00934","DOIUrl":"10.1016/j.btre.2025.e00934","url":null,"abstract":"<div><div>This study focused on enhancing the activity of the chitinase42 enzyme from <em>Trichoderma atroviride</em>. A Chitin-Binding Domain (ChBD) from <em>T. atroviride</em> chitinase18.10 was incorporated into the genomic DNA of the chitinase42 at the N-terminal using SOEing PCR. The engineered chimeric chitinase42 and the native chitinase42 were cloned into the expression vector pGDDEE, under the control of the synthetic inducible promoter SP-DDEE, resulting in constructs pGDDEENM1 and pGDDEEJN1, respectively. These were introduced into <em>Nicotiana benthamiana</em> using <em>Agrobacterium tumefaciens</em> strain 3101. Enzyme activity was optimized via colorimetric methods. Findings revealed optimal transient expression conditions: expression induction by spraying methyl jasmonate and sampling five days post- induction (5 DPI). The chimeric chitinase42 exhibited its highest enzymatic activity, surpassing chitinase42, at 40 °C and pH 4 with 1.55-fold higher than the native chitinase42 (lacking ChBD). Crucially, the chimeric chitinase42 demonstrated superior activity to the native enzyme, underscoring the potential for enhanced chitin degradation.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00934"},"PeriodicalIF":0.0,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362598","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":"A modified hot phenol-based protocol for high-purity Escherichia coli lipopolysaccharide extraction: Biochemical validation, stem cell cytotoxicity, and dose dependent multi-organ inflammation in a rat model","authors":"Edris Vahdani ,&nbsp;Ali Sepehrinezhad ,&nbsp;Elham Hosseini ,&nbsp;Saman Soleimanpour ,&nbsp;Sajad Sahab Negah ,&nbsp;Mohammad Ahanjan","doi":"10.1016/j.btre.2025.e00933","DOIUrl":"10.1016/j.btre.2025.e00933","url":null,"abstract":"<div><div>Gram-negative bacteria contain lipopolysaccharides (LPS) in their outer membrane, which induce strong inflammatory responses. Traditional LPS extraction methods often leave residual protein and nucleic acid contamination. These impurities interfere with downstream analyses and reduce reproducibility in biological studies. This study provides a modified hot phenol method combined with enzymatic treatments using proteinase K, DNase, RNase to extract pure LPS from <em>Escherichia coli</em>. Purity was confirmed by gel electrophoresis using Coomassie blue and silver nitrate staining. The biological activity of isolated LPS was tested on mesenchymal and embryonic neural stem cells, demonstrating decreased viability. In Wistar rats, LPS injection elevated serum IL-6 but not TNFα or IL-1β. Histological examinations indicated liver, kidney, brain, and colon tissue damage post-injection. Our results show that the modified hot phenol method efficiently produces high-purity, biologically active LPS suitable for both in vitro and in vivo inflammation studies, supporting research into inflammatory processes and associated diseases.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00933"},"PeriodicalIF":0.0,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362597","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":"Consolidated bioprocessing of inulin-containing feedstock to succinic acid by newly isolated Enterobacter sp. GAP1","authors":"Marcin Podleśny ,&nbsp;Tomasz Szymczak ,&nbsp;Jagoda Kucharska ,&nbsp;Monika Szymajda","doi":"10.1016/j.btre.2025.e00929","DOIUrl":"10.1016/j.btre.2025.e00929","url":null,"abstract":"<div><div>The novel <em>Enterobacter</em> sp. GAP1 strain was found to ferment inulin-containing carbohydrates in Jerusalem artichoke (JA) without the need for acidic or enzymatic pretreatment prior to fermentation. The GAP1 strain also possesses an efficient ability to produce succinic acid (SA). Using inulin as a carbon source in a liquid medium produced 29.4 g/L of SA. Using ground and dried JA tubers resulted in a SA concentration of 17.9 g/L, while adding freshly squeezed JA tuber juice resulted in a concentration of 24.7 g/L. In addition to tests using liquid media, the possibility of producing SA under conditions of limited water availability was also investigated, achieving a concentration of 27.7 g/L. Notably, the use of the <em>Enterobacter</em> sp. GAP1 strain is the first reported instance of a consolidated bioprocess for producing SA from inulin-containing materials both submerged and semi-solid state fermentation approach.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00929"},"PeriodicalIF":0.0,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362596","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":"Benchmarking long-read assembly tools and preprocessing strategies for bacterial genomes: A case study on E. coli DH5α","authors":"Megha S. Kumar ,&nbsp;Manoj Bhat Krishna ,&nbsp;K.P. Soman ,&nbsp;John Stanley ,&nbsp;Nader Pourmand ,&nbsp;Prashanth Suravajhala ,&nbsp;T.G.Satheesh Babu","doi":"10.1016/j.btre.2025.e00931","DOIUrl":"10.1016/j.btre.2025.e00931","url":null,"abstract":"<div><div>Genome assembly is a crucial step in microbial genomics, significantly impacting downstream applications such as functional annotation and comparative genomics. While long-read sequencing technologies have improved genome reconstruction, the choice of assembler and preprocessing methods substantially influences assembly quality. Genome assembly is a crucial step in microbial genomics, significantly impacting downstream applications such as functional annotation and comparative genomics. While long-read sequencing technologies have improved genome reconstruction, the choice of assembler and preprocessing methods substantially influences assembly quality. Here, we benchmarked eleven long-read assemblers—Canu, Flye, HINGE, Miniasm, NECAT, NextDenovo, Raven, Shasta, SmartDenovo, wtdbg2 (Redbean), and Unicycler—using standardized computational resources. Assemblies were evaluated on runtime, contiguity (N50, total length, contig count), GC content, and completeness using Benchmarking Universal Single-Copy Orthologs (BUSCO).</div><div>Assemblers employing progressive error correction with consensus refinement, notably NextDenovo and NECAT, consistently generated near-complete, single-contig assemblies with low misassemblies and stable performance across preprocessing types. Flye offered a strong balance of accuracy and contiguity, although it was sensitive to corrected input. Canu achieved high accuracy but produced fragmented assemblies (3–5 contigs) and required the longest runtimes. Unicycler reliably produced circular assemblies but with slightly shorter contigs than Flye or NextDenovo. Ultrafast tools such as Miniasm and Shasta provided rapid draft assemblies, yet were highly dependent on preprocessing and required polishing to achieve completeness. HINGE and wtdbg2 underperformed due to structural instability and fragmentation.</div><div>Preprocessing had a marked effect: filtering improved genome fraction and BUSCO completeness, trimming reduced low-quality artifacts, and correction benefited OLC-based assemblers but occasionally increased misassemblies in graph-based tools. Overall, assembler choice and preprocessing jointly determine accuracy, contiguity, and computational efficiency. These results provide a reproducible framework for selecting assembly pipelines in prokaryotic genomics, underscoring that no single assembler is universally optimal.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00931"},"PeriodicalIF":0.0,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332693","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":"Improving a photosynthetic bioprocess with a ubiquitous additive: Using clay powder in the cultivation of Rhodopseudomonas palustris","authors":"Sheida Stephens ,&nbsp;Mona Abo-Hashesh ,&nbsp;Radhakrishnan Mahadevan ,&nbsp;D. Grant Allen","doi":"10.1016/j.btre.2025.e00930","DOIUrl":"10.1016/j.btre.2025.e00930","url":null,"abstract":"<div><div>A key challenge in process optimization is reactor performance, particularly in light-dependent bioprocesses. While novel photobioreactor designs exist, adapting established bioreactors with simple media supplementation may provide a more practical and modular alternative to complex mechanical modifications. In this study, we evaluated the effect of supplementing 0.2 % (w/v) clay powder on acetate production by <em>Rhodopseudomonas palustris</em> grown on butyrate. Among the clay types tested, kaolin showed the most pronounced benefits, with acetate accumulation increasing by 45 % relative to controls. These improvements are attributed to a combination of enhanced light distribution and increased cellular aggregation. Photosynthetic photon flux density measurements confirmed that kaolin reduced the extent of cellular shading by increasing light scattering within the culture. Taken together, these findings demonstrate that supplementation with a widely available clay can improve light penetration in suspended phototrophic cultures, offering a novel andaccessible strategy for optimizing photosynthetic bioprocesses.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00930"},"PeriodicalIF":0.0,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332691","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":"Sustainable fuel and power from biomass: 4E analysis of a solar-assisted DME production system with CO₂ capture","authors":"Atieh Kermani ,&nbsp;Farzin Hosseinifard ,&nbsp;Mohsen Salimi ,&nbsp;Majid Amidpour","doi":"10.1016/j.btre.2025.e00928","DOIUrl":"10.1016/j.btre.2025.e00928","url":null,"abstract":"<div><div>Transitioning to clean energy requires efficient, low-carbon fuel production methods. Traditional biomass-to-fuel approaches are limited by inefficiency, cost, and emissions. This study presents an innovative system based on renewable lignocellulosic biomass to produce dimethyl ether (DME), methanol, and electricity simultaneously. The design integrates thermochemical conversion, solar thermal energy, internal power generation, and post-combustion CO₂ capture. Waste heat and solar energy drive dual electricity-producing loops, enabling internal energy sufficiency and surplus sale. Simulations indicate 50 % total energy efficiency and 49 % exergy efficiency, with hourly production of 2.7 tons DME and 0.56 tons methanol. Economic analysis shows baseline feasibility with an NPV of ∼$530 M and payback period ∼5.5 years; sensitivity to biomass price, capital cost, and discount rate is noted, highlighting potential uncertainty ranges. This integrated pathway offers a scalable, low-carbon, and economically viable solution for sustainable bioenergy.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00928"},"PeriodicalIF":0.0,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219780","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":"Glycoengineering of plant-produced Pembrolizumab enhances FcRn binding and extends serum half-life in mice","authors":"Christine Joy I. Bulaon ,&nbsp;Janejira Jaratsittisin ,&nbsp;Kaewta Rattanapisit ,&nbsp;Pipob Suwanchaikasem ,&nbsp;Shiying Guo ,&nbsp;Khwanchit Boonha ,&nbsp;Pannamthip Pitaksajjakul ,&nbsp;Nipaporn Simsom ,&nbsp;Vudhiporn Limprasutr ,&nbsp;Waranyoo Phoolcharoen","doi":"10.1016/j.btre.2025.e00927","DOIUrl":"10.1016/j.btre.2025.e00927","url":null,"abstract":"<div><div>Plant systems offer scalable and cost-effective platforms for antibody production, but plant-specific glycans may affect pharmacokinetics and immunogenicity. To evaluate the impact of Fc glycosylation, four Pembrolizumab glycovariants were generated in <em>Nicotiana benthamiana</em>: wild-type glycosylation (Pembro-WT), high-mannose with SEKDEL (Pembro-KD), aglycosylated N297A mutant (Pembro-NG), and a core fucose/xylose-deficient variant (Pembro-XF). Glycoproteins were transiently expressed either in wild-type or ΔXF plants, purified, and characterized for glycan composition, in vitro binding, and in vivo pharmacokinetics. LC-MS confirmed distinct glycoform patterns, while PD-1 binding was retained across all variants. Pembro-XF showed the highest FcRn binding affinity and longest serum half-life (45.83 h) in mice, compared to Pembro-WT (26.7 h), Pembro-KD (32.95 h), Pembro-NG (34.27 h), and Keytruda® (33.26 h). As an initial efficacy evaluation, Pembro-WT demonstrated strong antitumor activity in a murine colon cancer model. These findings support plant glycoengineering as a strategy to enhance antibody pharmacokinetics and advance next generation antibody therapeutics.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00927"},"PeriodicalIF":0.0,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219779","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}