BioTech最新文献

{"title":"Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights.","authors":"Jiawei Chen, Ravi Potlapalli, Heng Quan, Lingtao Chen, Ying Xie, Seyedamin Pouriyeh, Nazmus Sakib, Lichao Liu, Yixin Xie","doi":"10.3390/biotech13010003","DOIUrl":"10.3390/biotech13010003","url":null,"abstract":"<p><p>DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10801582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513707","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}

{"title":"Styrene Production in Genetically Engineered <i>Escherichia coli</i> in a Two-Phase Culture.","authors":"Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo","doi":"10.3390/biotech13010002","DOIUrl":"10.3390/biotech13010002","url":null,"abstract":"<p><p>Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered <i>Escherichia coli</i>. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from <i>Arabidopsis thaliana</i> (AtPAL) and <i>Brachypodium distachyon</i> (BdPAL) for their ability to produce <i>trans</i>-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing <i>E. coli</i> produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an <i>E. coli</i> strain that co-expressed AtPAL2 and ferulic acid decarboxylase from <i>Saccharomyces cerevisiae</i>. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10801462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513708","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}

{"title":"Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care","authors":"Marian L. Henderson, Jacob K. Zieba, Xiaopeng Li, Daniel B. Campbell, Michael R. Williams, Daniel L. Vogt, Caleb P. Bupp, Yvonne Edgerly, S. Rajasekaran, Nicholas L. Hartog, Jeremy Prokop, Jena M. Krueger","doi":"10.3390/biotech13010001","DOIUrl":"https://doi.org/10.3390/biotech13010001","url":null,"abstract":"Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost–benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"39 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139451947","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":"Biocatalysts Based on Immobilized Lipases for the Production of Fatty Acid Ethyl Esters: Enhancement of Activity through Ionic Additives and Ion Exchange Supports.","authors":"Juan S Pardo-Tamayo, Sebastián Arteaga-Collazos, Laura C Domínguez-Hoyos, César A Godoy","doi":"10.3390/biotech12040067","DOIUrl":"10.3390/biotech12040067","url":null,"abstract":"<p><p>Ionic additives affect the structure, activity and stability of lipases, which allow for solving common application challenges, such as preventing the formation of protein aggregates or strengthening enzyme-support binding, preventing their desorption in organic media. This work aimed to design a biocatalyst, based on lipase improved by the addition of ionic additives, applicable in the production of ethyl esters of fatty acids (EE). Industrial enzymes from <i>Thermomyces lanuginosus</i> (TLL), <i>Rhizomucor miehei</i> (RML), <i>Candida antárctica B</i> (CALB) and Lecitase^®, immobilized in commercial supports like Lewatit^®, Purolite^® and Q-Sepharose^®, were tested. The best combination was achieved by immobilizing lipase TLL onto Q-Sepharose^® as it surpassed, in terms of %EE (70.1%), the commercial biocatalyst Novozyme^® 435 (52.7%) and was similar to that of Lipozyme TL IM (71.3%). Hence, the impact of ionic additives like polymers and surfactants on both free and immobilized TLL on Q-Sepharose^® was assessed. It was observed that, when immobilized, in the presence of sodium dodecyl sulfate (SDS), the TLL derivative exhibited a significantly higher activity, with a 93-fold increase (1.02 IU), compared to the free enzyme under identical conditions (0.011 IU). In fatty acids ethyl esters synthesis, Q-SDS-TLL novel derivatives achieved results similar to commercial biocatalysts using up to ~82 times less enzyme (1 mg/g). This creates an opportunity to develop biocatalysts with reduced enzyme consumption, a factor often associated with higher production costs. Such advancements would ease their integration into the biodiesel industry, fostering a greener production approach compared to conventional methods.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10742180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138831956","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}

{"title":"Gibberellin-Producing Bacteria Isolated from Coastal Soil Enhance Seed Germination of Mallow and Broccoli Plants under Saline Conditions.","authors":"Ji-In Woo, Md Injamum-Ul-Hoque, Nazree Zainurin, Shifa Shaffique, Eun-Hae Kwon, Ho-Jun Gam, Jin Ryeol Jeon, In-Jung Lee, Gil-Jae Joo, Sang-Mo Kang","doi":"10.3390/biotech12040066","DOIUrl":"10.3390/biotech12040066","url":null,"abstract":"<p><p>Salinity hinders plant growth, posing a substantial challenge to sustainable agricultural yield maintenance. The application of plant growth-promoting rhizobacteria (PGPR) offers an emerging strategy to mitigate the detrimental effects of high salinity levels. This study aimed to isolate and identify gibberellin-producing bacteria and their impact on the seed germination of <i>Malva verticillata</i> (mallow) and <i>Brassica oleracea var. italica</i> (broccoli) under salt stress. In this study, seven bacterial isolates (KW01, KW02, KW03, KW04, KW05, KW06, and KW07) were used to assess their capacity for producing various growth-promoting traits and their tolerance to varying amounts of salinity (100 mM and 150 Mm NaCl). The findings revealed that KW05 and KW07 isolates outperformed other isolates in synthesizing indole-3-acetic acid, siderophores, and exopolysaccharides and in solubilizing phosphates. These isolates also enhanced phosphatase activity and antioxidant levels, including superoxide dismutase and catalase. Both KW05 and KW07 isolate highlight the growth-promoting effects of gibberellin by enhancing of growth parameters of Waito-C rice. Further, gas chromatography-mass spectrometry validation confirmed the ability of KW05 and KW07 to produce gibberellins (GAs), including GA₁, GA₃, GA₄, and GA₇. Seed germination metrics were enhanced due to the inoculation of KW05 and KW07. Moreover, inoculation with KW05 increased the fresh weight (FW) (7.82%) and total length (38.61%) of mallow under salt stress. Inoculation with KW07 increased the FW (32.04%) and shoot length of mallow under salt stress. A single inoculation of these two isolates increased broccoli plants' FW and shoot length under salt stress. Gibberellin-producing bacteria helps in plant growth promotion by improving salt tolerance by stimulating root elongation and facilitating enhanced absorption of water and nutrient uptake in salty environments. Based on these findings, they can play a role in boosting agricultural yield in salt-affected areas, which would help to ensure the long-term viability of agriculture in coastal regions.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10741878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138831957","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}

{"title":"Detection and Characterization of Electrogenic Bacteria from Soils","authors":"Ana Rumora, Liliana Hopkins, Kayla Yim, Melissa F. Baykus, Luisa Martinez, Luis Jimenez","doi":"10.3390/biotech12040065","DOIUrl":"https://doi.org/10.3390/biotech12040065","url":null,"abstract":"Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35–37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 109 electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"81 26","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138606199","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":"Fungicide Resistance in <i>Botrytis</i> spp. and Regional Strategies for Its Management in Northern European Strawberry Production.","authors":"Roland W S Weber, Antonios Petridis","doi":"10.3390/biotech12040064","DOIUrl":"10.3390/biotech12040064","url":null,"abstract":"<p><p>Grey mould, caused by <i>Botrytis cinerea</i> and other <i>Botrytis</i> spp., is a major cause of fruit rot in strawberries and other fruit crops worldwide. Repeated fungicide applications are essential in order to secure harvests. However, resistance to all currently registered single-site fungicides is widespread. The rising importance of strains with multiple resistance to most or all fungicides is of particular concern. These strains may be introduced into fields via contaminated nursery plants and/or by immigration from adjacent plots. On the basis of research conducted in northern German and Danish strawberry production, a concept to manage fungicide resistance under northern European conditions has been developed and put into regional strawberry production practice. This principally includes the testing of nursery plants for fungicide-resistant <i>Botrytis</i> strains prior to planting; the restricted and specific use of fungicides at flowering in the production fields, taking account of the resistance spectrum within the local <i>Botrytis</i> population; and crop sanitation measures such as the removal of rotting fruits at the beginning of harvest. Further options such as protected cultivation, reduced fertilisation and biological control are also discussed. The practical implementation of such a strategy in northern Germany and Denmark has been shown to reduce the occurrence of multi-resistant strains to a tolerable steady-state level.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10660734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138177404","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}

{"title":"The Controversial Nature of Some Non-Starter Lactic Acid Bacteria Actively Participating in Cheese Ripening","authors":"Svetoslav G. Dimov","doi":"10.3390/biotech12040063","DOIUrl":"https://doi.org/10.3390/biotech12040063","url":null,"abstract":"This mini review deals with some controversial non-starter lactic acid bacteria (NSLAB) species known to be both human and animal pathogens but also health-promoting and probiotic. The focus is on Lactococcus garvieae, two Streptococcus species (S. uberis and S. parauberis), four Weissella species (W. hellenica, W. confusa, W. paramesenteroides, and W. cibaria), and Mammalicoccus sciuri, which worldwide, are often found within the microbiotas of different kinds of cheese, mainly traditional artisanal cheeses made from raw milk and/or relying on environmental bacteria for their ripening. Based on literature data, the virulence and health-promoting effects of these bacteria are examined, and some of the mechanisms of these actions are reviewed. Additionally, their possible roles in cheese ripening are also discussed. The analysis of the literature data available so far showed that, in general, the pathogenic and the beneficial strains, despite belonging to the same species, show somewhat different genetic constitutions. Yet, when the safety of a given strain is assessed, genomic analysis on its own is not enough, and a polyphasic approach including additional physiological and functional tests is needed.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":" 38","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135241748","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":"Tracking of Systemic Lupus Erythematosus (SLE) Longitudinally Using Biosensor and Patient-Reported Data: A Report on the Fully Decentralized Mobile Study to Measure and Predict Lupus Disease Activity Using Digital Signals—The OASIS Study","authors":"Eldon R. Jupe, Gerald H. Lushington, Mohan Purushothaman, Fabricio Pautasso, Georg Armstrong, Arif Sorathia, Jessica Crawley, Vijay R. Nadipelli, Bernard Rubin, Ryan Newhardt, Melissa E. Munroe, Brett Adelman","doi":"10.3390/biotech12040062","DOIUrl":"https://doi.org/10.3390/biotech12040062","url":null,"abstract":"(1) Objective: Systemic lupus erythematosus (SLE) is a complex disease involving immune dysregulation, episodic flares, and poor quality of life (QOL). For a decentralized digital study of SLE patients, machine learning was used to assess patient-reported outcomes (PROs), QOL, and biometric data for predicting possible disease flares. (2) Methods: Participants were recruited from the LupusCorner online community. Adults self-reporting an SLE diagnosis were consented and given a mobile application to record patient profile (PP), PRO, and QOL metrics, and enlisted participants received smartwatches for digital biometric monitoring. The resulting data were profiled using feature selection and classification algorithms. (3) Results: 550 participants completed digital surveys, 144 (26%) agreed to wear smartwatches, and medical records (MRs) were obtained for 68. Mining of PP, PRO, QOL, and biometric data yielded a 26-feature model for classifying participants according to MR-identified disease flare risk. ROC curves significantly distinguished true from false positives (ten-fold cross-validation: p < 0.00023; five-fold: p < 0.00022). A 25-feature Bayesian model enabled time-variant prediction of participant-reported possible flares (P(true) > 0.85, p < 0.001; P(nonflare) > 0.83, p < 0.0001). (4) Conclusions: Regular profiling of patient well-being and biometric activity may support proactive screening for circumstances warranting clinical assessment.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":" 9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135286113","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":"Bacterial Proteases as Potentially Exploitable Modulators of SARS-CoV-2 Infection: Logic from the Literature, Informatics, and Inspiration from the Dog","authors":"Gerald H. Lushington, Annika Linde, Tonatiuh Melgarejo","doi":"10.3390/biotech12040061","DOIUrl":"https://doi.org/10.3390/biotech12040061","url":null,"abstract":"(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the Pseudomonadales genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated Moraxella fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that Moraxella bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"28 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136103807","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}