{"title":"The landscape of LncRNAs in diabetic kidney disease: a meta-analysis of transcriptomics data","authors":"Raziyeh Rezaei , Basireh Bahrami , Yousof Gheisari","doi":"10.1016/j.crbiot.2025.100322","DOIUrl":"10.1016/j.crbiot.2025.100322","url":null,"abstract":"<div><div>Non-coding regions of the genome are known to influence complex disorders, yet the role of long non-coding RNAs (lncRNAs) in Diabetic Kidney Disease (DKD) remains underexplored. This study conducts a meta-analysis of RNA-sequencing data from murine kidney samples of type 1 (T1DM) and type 2 diabetes mellitus (T2DM) to identify lncRNAs associated with DKD. DKD-associated datasets were harvested, and after data pre-processing and quality assessment, 6 T1DM and 4 T2DM datasets were included. Data integration, batch correction, and normalization were performed, followed by the identification of differentially expressed lncRNAs (meta-DELs) and mRNAs (meta-DEMs). A DKD mouse model was developed to validate the expression of selected meta-DELs using qRT-PCR. The meta-analysis identified 188 meta-DELs in T1DM and 68 in T2DM. Notably, a small set of lncRNAs have dense mRNA interactions, including <em>Dancer</em>, <em>Gm7628</em>, <em>C4a</em>, and <em>Gm17300</em> in T1DM and <em>Malat1</em>, <em>C4a</em>, <em>Gm17300</em>, and <em>Eif4a2</em> in T2DM. Expression analysis confirmed the up-regulation of seven selected meta-DELs in the DKD model, with Trp53cor1, Gm15462, and Gm42664 reaching statistical significance. This systematic analysis of high-quality expression profiles identified meta-DELs consistently associated with DKD, distinguishing actual lncRNA changes from those influenced by experimental conditions or gene expression noise.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100322"},"PeriodicalIF":4.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003841","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}
Zuhra Bibi , Dilara Abbas Bukhari , Muhammad Qadeer Sarwar , Arifullah , Samina Younas , Tayyab Manzoor , Abdul Rehman
{"title":"Gut health improvement by locally isolated probiotics and histomorphometric analysis in Wistar rats","authors":"Zuhra Bibi , Dilara Abbas Bukhari , Muhammad Qadeer Sarwar , Arifullah , Samina Younas , Tayyab Manzoor , Abdul Rehman","doi":"10.1016/j.crbiot.2024.100271","DOIUrl":"10.1016/j.crbiot.2024.100271","url":null,"abstract":"<div><div>In the present investigation, lab-isolated probiotics <em>Weisella confusa</em> MZ735961.1, <em>Lactiplantibacillus plantarum</em> MZ707748.1<em>, L. plantarum</em> MZ710117.1<em>,</em> and <em>L. plantarum</em> MZ735961 were used separately and in combinations to evaluate their effect on gut morphology of Wistar rats. Synergistic groups were formed by 1:1 and labeled as G1 (<em>L. plantarum</em> MZ707748.1 and <em>L. plantarum</em> MZ729681.1), G2 (<em>W. confusa</em> MZ735961.1 and <em>L. plantarum</em> MZ727611.1), G3 (<em>L. plantarum</em> MZ729681.1, <em>W. confusa</em> MZ735961.1, and <em>Lactobacillus acidophilus</em> La-14), G4 (all above mentioned probiotics). Rats were gavage-fed with probiotics according to their colony-forming unit (CFU). The experiment was carried out for 35 days. The bacteria were re-isolated from the gut and identified by biochemical tests which confirmed the administration and re-isolation of different <em>Lactobacillus</em> strains from the gut. Molecular characterization was done through 16S rRNA by using universal primers. After sequencing eight <em>Lactobacillus</em> strains were identified. Histopathology of rats’ intestines was done, and different parameters were examined. Villus height, crypt height, crypt width, mucosa, and sub-mucosa of jejunum were significantly (p = 0.00) increased in the G3 synergetic probiotic group compared to 0-day and negative control. However, the villus width showed non-significant (p > 0.05) variations in both genders. Mucosa tunic, muscle tunic, total wall, and crypt depth were significantly increased (p = 0.00) in the G4 group of medial colon. The study concluded that gut morphology improves as probiotics adhere better to the intestinal epithelium, excluding pathogens, reducing inflammation, enhancing nutrient absorption, and stimulating mucosal growth. This results in improved villus structure and gut wall integrity.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"9 ","pages":"Article 100271"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143136459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rifat Zubair Ahmed , Ashraful Islam , Tiantian Tian , Zhe Tian , Yu Zhang , Min Yang
{"title":"Validation of microbial source tracking markers through PCR-based molecular analysis and microbial genome database","authors":"Rifat Zubair Ahmed , Ashraful Islam , Tiantian Tian , Zhe Tian , Yu Zhang , Min Yang","doi":"10.1016/j.crbiot.2025.100304","DOIUrl":"10.1016/j.crbiot.2025.100304","url":null,"abstract":"<div><div>Microbial Source Tracking (MST) uses molecular markers targeting host-associated gut microorganisms to identify fecal pollution. However, MST faces significant challenges in fecal source identification, particularly due to the markers’ poor specificity and shared genomic areas among microorganisms from different host sources. This study addresses these challenges by using host-specific <em>Escherichia coli</em> genetic markers, originally developed through a novel, library-independent approach, to detect sources of fecal pollution. A total of 563 <em>E.coli</em> isolates from chicken, cow, and pig feces were isolated and assessed by nine reported host-associated <em>E. coli</em> genetic markers (Chicken: CH7, CH9, CH12, CH13; Cow: CO2, CO3; Pig: P1, P3, P4) through PCR. Marker possession patterns, sensitivity, specificity, and accuracy were calculated. The NCBI Microbial Genome database was searched for sequences homologous to genome regions of studied genetic markers and evaluated by finding the percentage of host sources and sequence location in the genome. Homology evaluation with binary PCR results was used to predict the best-performing marker. PCR results exhibited that the most effective markers were chicken CH7 (67% sensitivity, 77.9% specificity, 74.4% accuracy) and CH9 (55% sensitivity, 99.4% specificity, 84.7% accuracy). However, a homology search in the database narrowed the selection of the top-performing marker to CH7, which showed homology with <em>E.coli</em> from chicken hosts, while other markers exhibited higher homology with <em>E.coli</em> from Humans. Furthermore, sequences from the database homologous to the CH9 and CO2 markers were found on a plasmid, while those for CH12, CO3, P1, and P4 were on the chromosome, and CH7, CH13, and P3 were on both. This study highlights the critical need for integrated approaches to assess molecular markers in MST assays, emphasizing their significance in advancing research within the field.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100304"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212018","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}
Marcela Guimarães , Daniela Luz , Elisabeth de Fátima Pires Augusto , Lucia Vieira , Maricilia Silva Costa , Roxane Maria Fontes Piazza , José Geraldo da Cruz Pradella
{"title":"Cost-effective production process of scFv antibody fragments against Shiga toxin 2 via recombinant E. coli","authors":"Marcela Guimarães , Daniela Luz , Elisabeth de Fátima Pires Augusto , Lucia Vieira , Maricilia Silva Costa , Roxane Maria Fontes Piazza , José Geraldo da Cruz Pradella","doi":"10.1016/j.crbiot.2025.100310","DOIUrl":"10.1016/j.crbiot.2025.100310","url":null,"abstract":"<div><div>Shiga toxin (Stx)-producing <em>Escherichia coli</em> (STEC) and its subgroup enterohemorrhagic <em>E. coli</em> are significant pathogens responsible for diarrhea, which can progress to hemorrhagic colitis and hemolytic uremic syndrome (HUS), the leading cause of acute renal failure in children. Early diagnosis is crucial for effective clinical management, as antibiotic treatment is not recommended for STEC infections. The present study aimed to establish a cost-effective biotechnological platform for cultivating recombinant <em>E. coli</em> to produce scFv antibody fragments against Stx2 for diagnostic applications. The method was first evaluated through shake flask experiments and subsequently scaled up to bench-scale bioreactors operated in both batch and fed-batch modes using defined culture media. Optimal production conditions were achieved by inducing recombinant <em>E. coli</em> pLys at 18 °C for 18 h with 0.1 mM IPTG, resulting in a yield of 3.0 to 4.0 mg scFv/g cell biomass. A fed-batch, high-cell-density procedure with <em>E. coli</em> pLysS achieved a maximum production up to 150 mg scFv/L. A preliminary economic assessment demonstrated the production potential at a value of around $250/g scFv. Economic analysis also highlights that the relative cost of capital investment becomes important as production processes intensify. Therefore, technical parameters such as productivity (scFv mass/bioreactor volume * time) and scFv concentration (mass scFv mass/bioreactor volume) should be prioritized to maximize their values. Similarly, optimization of the recombinant <em>E. coli</em> microbial platform should be pursued to increase the Yp/x level.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100310"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144549698","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}
Husnain Ahmad Khan , Shahid Sher , Dilara Abbas Bukhari , Abdul Rehman
{"title":"Bioremediation of heavy metals from electronic waste dumping sites with bacteria","authors":"Husnain Ahmad Khan , Shahid Sher , Dilara Abbas Bukhari , Abdul Rehman","doi":"10.1016/j.crbiot.2025.100309","DOIUrl":"10.1016/j.crbiot.2025.100309","url":null,"abstract":"<div><div>Samples were collected from two e-waste dumping sites (Mehmood Booti (31°36′28″N, 74°23′36″E) and Lakhodair (31°37′36.6″ N, 74°25′07.6″ E)) in Lahore, Pakistan. A portable multiparameter was used to determine physicochemical parameters such as temperature, pH, electrical conductivity, turbidity, total suspended particles, and total dissolved solids. Minimal salt broth was used for the determination of the minimal inhibitory concentration of the bacterium against all heavy metals. Bacterial morphology was observed under a scanning electron microscope with and without metal stress. The temperature range for all these samples was 28.7 to 35.7 °C, while the pH range was 6.7 to 7.89. The other parameters range, such as electrical conductivity µS/cm (698–8742), turbidity (14.2–103), total suspended particles (31–698), and total dissolved solids (564–23456). The lead concentration in the Mehmood Booti soil sample was 1800 mg/kg, while in the Lakhodair soil, it was 1567 mg/kg. <em>Microbacterium</em> sp. strain 1S1 was utilized for bioremediation assay at the lab and pilot scale. The resistance capacity of this bacterium against different metals was in the following order: As > Pb > Cd > Cu > Cr > Ni. The bioremediation potential of the bacterium against arsenic was 81.33 % and 96 % after 2 and 4 days. The least activity was observed against nickel, which was 17 and 28.33 % after 2 and 4 days. The metal removal capacity per CFU was the maximum for lead and arsenic compared to other metals, which were 1.99E-7 and 1.45E-07. The heat-inactivated bacterial cells removed arsenic in higher concentrations and lead in lower concentrations. The electron microscopy showed no significant alteration in bacterial morphology in control and metal-treated bacterial cells. The nanopore long-read sequencing analysis revealed that cadmium, nickel, copper, and arsenic resistance genes were found on the bacterial genome. No genes were found for lead and chromium but 849 hypothetical coding sequences having unknown functions were present on the bacterial genome. So, the <em>Microbacterium</em> sp. strain 1S1 is a potential candidate for the removal of heavy metals from e-waste dumping sites.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100309"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366627","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}
Khouloud Zribi , Matteo Ciciani , Agata Sofia Assunção Carreira , Martina Paganin , Sara Pozzo , Lucio Cinà , Baris Binay , Francesco Secundo , Nicola Segata , Alessandro Provenzani
{"title":"Characterization of a novel thermostable NAD+-dependent formate dehydrogenase from Methylacidiphilum kamchatkense Kam1 (MkaFDH)","authors":"Khouloud Zribi , Matteo Ciciani , Agata Sofia Assunção Carreira , Martina Paganin , Sara Pozzo , Lucio Cinà , Baris Binay , Francesco Secundo , Nicola Segata , Alessandro Provenzani","doi":"10.1016/j.crbiot.2025.100306","DOIUrl":"10.1016/j.crbiot.2025.100306","url":null,"abstract":"<div><div>Metal-independent NAD<sup>+</sup>-dependent formate dehydrogenases (FDHs) are enzymes responsible for catalyzing the conversion of formate (HCOO<sup>–</sup>) to carbon dioxide (CO<sub>2</sub>), a biological reaction involved in microbial carbon processing and cofactor regeneration. These enzymes show large potential for environmental bioremediation and biotechnological uses. However, FDHs applications are hampered by the enzymes’ limited stability under extreme conditions, such as high temperatures or extreme pH. Therefore, we aimed to identify and characterize novel metal-independent FDHs with improved activity and thermostability compared to known FDHs. By using four different FDH protein sequences, <em>Ct</em>FDH (from <em>Chaetomium thermophilum)</em>, <em>Mt</em>FDH (from <em>Myceliophthora thermophile)</em>, <em>Op</em>FDH (from <em>Ogata parapolymorpha</em> DL-1) and <em>Pse</em>FDH (from <em>Pseudomonas</em> sp.<em>101)</em> we retrieved 18,850 FDHs sequences from the NCBI database and matched against the species present in the database of thermophilic bacteria, ThermoBase. Our phylogenetic analysis identified four distinct FDHs in thermophilic bacteria: <em>Methylocaldum szegediense</em> (<em>Msz</em>FDH), <em>Methylacidiphilum kamchatkense</em> (<em>Mka</em>FDH), <em>Mycobacterium arosiense</em> (<em>Mar</em>FDH) and <em>Mycobacterium genavense</em> (<em>Mge</em>FDH). We selected and characterized the <em>Mka</em>FDH as it was expressed in the thermophilic bacterium with the highest optimum growth (55 °C) among the four bacteria. The <em>MkaFDH</em> was cloned, and the recombinant protein was expressed in <em>E. coli</em> and purified. The conditions for the optimal catalytic activity for formate oxidations were screened and identified, revealing metal-independent, NAD<sup>+</sup>-restricted activity in phosphate buffer, pH 8. Importantly, the enzyme showed remarkable thermal stability and catalytic activity, showing a melting temperature (Tm) of 60.15 °C, as confirmed by far-UV circular dichroism (CD). Finally, the enzyme showed good thermostability for formate oxidation up to 57.5 °C, and its high catalytic efficiency (k<sub>cat</sub>/K<sub>m</sub> = 0.44 s<sup>−1</sup>mM<sup>−1</sup>) suggested its potential industrial application. Collectively, we describe here a novel FDH with relevant thermostability that can be exploited as a prototype for industrial applications.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100306"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366626","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}
Marko Tesanovic , Torben Bardel , Robin Karl , Sonja Berensmeier
{"title":"Towards a digital twin: Digitization and model-based optimization of the innovative high-gradient magnetic separator","authors":"Marko Tesanovic , Torben Bardel , Robin Karl , Sonja Berensmeier","doi":"10.1016/j.crbiot.2025.100324","DOIUrl":"10.1016/j.crbiot.2025.100324","url":null,"abstract":"<div><div>Downstream processing in biotechnology relies on multiple unit operations to achieve high product purity, driving up costs, time, and yield losses. High-Gradient Magnetic Separation (HGMS) offers a promising alternative by consolidating steps and enabling direct target capture from complex media. However, its industrial adoption is hindered by suboptimal performance, limited scalability, and insufficient automation for reproducibility. Furthermore, process efficiency is often not fully realized due to the reliance on fixed operational recipes.</div><div>This study presents a digital twin framework for a pilot-scale HGMS system, integrating real-time monitoring, automated control, advanced mechanistic models, and multi-objective optimization using Bayesian algorithms. The framework was validated for robustness, scalable data handling, and predictive control. Key contributions include the development of soft sensors, automated control strategies for improved reproducibility, in-silico optimization of a human Immunoglobulin G (hIgG) capture process — a monoclonal antibody broadly relevant in biopharmaceutical applications — with real-time pH adjustment, and a sensitivity analysis of objective weights, revealing trade-offs between yield, resource use, and processing time. Optimization results indicated a theoretical 4% productivity gain and a 3 percentage point yield improvement, while exposing critical design constraints in the HGMS chamber.</div><div>These findings underscore the potential of digital twins to accelerate process optimization and reduce development costs through in-silico experimentation. Future work will focus on refining identified design limitations and extending the framework to optimize process conditions for diverse bioproducts, enhancing scalability and efficiency.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100324"},"PeriodicalIF":4.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810587","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":"Corrigendum to “A review: Anti-obesity drug discovery from natural plant metabolites and endogenous peptides” [Curr. Res. Biotechnol. 8 (2024) 100259]","authors":"Xiaomu Zhu , Dongdong Wang , Atanas G. Atanasov","doi":"10.1016/j.crbiot.2025.100289","DOIUrl":"10.1016/j.crbiot.2025.100289","url":null,"abstract":"","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"9 ","pages":"Article 100289"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143834803","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}