BioTech最新文献

{"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}

{"title":"Shikonin and Juglone Inhibit <i>Mycobacterium tuberculosis</i> Low-Molecular-Weight Protein Tyrosine Phosphatase a (Mt-PTPa).","authors":"Abdulhakeem O Sulyman,&nbsp;Jessie Fulcher,&nbsp;Samuel Crossley,&nbsp;Amos A Fatokun,&nbsp;Femi J Olorunniji","doi":"10.3390/biotech12030059","DOIUrl":"https://doi.org/10.3390/biotech12030059","url":null,"abstract":"<p><p>Low-molecular-weight protein tyrosine phosphatases (LMW-PTPs) are involved in promoting the intracellular survival of <i>Mycobacterium tuberculosis</i> (Mtb), the causative organism of tuberculosis. These PTPs directly alter host signalling pathways to evade the hostile environment of macrophages and avoid host clearance. Among these, protein tyrosine phosphatase A (Mt-PTPa) is implicated in phagosome acidification failure, thereby inhibiting phagosome maturation to promote <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) survival. In this study, we explored Mt-PTPa as a potential drug target for treating <i>Mtb</i>. We started by screening a library of 502 pure natural compounds against the activities of Mt-PTPa in vitro, with a threshold of 50% inhibition of activity via a <500 µM concentration of the candidate drugs. The initial screen identified epigallocatechin, myricetin, rosmarinic acid, and shikonin as hits. Among these, the naphthoquinone, shikonin (5, 8-dihydroxy-2-[(1R)-1-hydroxy-4-methyl-3-pentenyl]-1,4-naphthoquinone), showed the strongest inhibition (IC₅₀ 33 µM). Further tests showed that juglone (5-hydroxy-1,4-naphthalenedione), another naphthoquinone, displayed similar potent inhibition of Mt-PTPa to shikonin. Kinetic analysis of the inhibition patterns suggests a non-competitive inhibition mechanism for both compounds, with inhibitor constants (Ki) of 8.5 µM and 12.5 µM for shikonin and juglone, respectively. Our findings are consistent with earlier studies suggesting that Mt-PTPa is susceptible to specific allosteric modulation via a non-competitive or mixed inhibition mechanism.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10526854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151111","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":"Assessing Curcumin Uptake and Clearance and Their Influence on Superoxide Dismutase Activity in <i>Drosophila melanogaster</i>.","authors":"Tammy R Hoffman,&nbsp;Sarah A Emsley,&nbsp;Jenna C Douglas,&nbsp;Kaela R Reed,&nbsp;Abigail R Esquivel,&nbsp;Marc J Koyack,&nbsp;Brie E Paddock,&nbsp;Patrick Videau","doi":"10.3390/biotech12030058","DOIUrl":"https://doi.org/10.3390/biotech12030058","url":null,"abstract":"<p><p>While normal levels of reactive oxygen and nitrogen species (RONS) are required for proper organismal function, increased levels result in oxidative stress. Oxidative stress may be managed via the scavenging activities of antioxidants (e.g., curcumin) and the action of enzymes, including superoxide dismutase (SOD). In this work, the uptake and clearance of dietary curcuminoids (consisting of curcumin, demethoxycurcumin, and bisdemethoxycurcumin) was assessed in <i>Drosophila melanogaster</i> larvae following chronic or acute exposure. High levels of curcuminoid uptake and loss were observed within a few hours and leveled off within eight hours post treatment onset. The addition or removal of curcuminoids from media resulted in corresponding changes in SOD activity, and the involvement of each of the three <i>SOD</i> genes was assessed for their contribution to total SOD activity. Taken together, these data provide insight into the uptake and clearance dynamics of curcuminoids and indicate that, while SOD activity generally increases following curcuminoid treatment, the individual <i>SOD</i> genes appear to contribute differently to this response.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10526445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41150717","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":"Targeted Strategies for Degradation of Key Transmembrane Proteins in Cancer.","authors":"Vehary Sakanyan,&nbsp;Nina Iradyan,&nbsp;Rodolphe Alves de Sousa","doi":"10.3390/biotech12030057","DOIUrl":"https://doi.org/10.3390/biotech12030057","url":null,"abstract":"<p><p>Targeted protein degradation is an attractive technology for cancer treatment due to its ability to overcome the unpredictability of the small molecule inhibitors that cause resistance mutations. In recent years, various targeted protein degradation strategies have been developed based on the ubiquitin-proteasome system in the cytoplasm or the autophagy-lysosomal system during endocytosis. In this review, we describe and compare technologies for the targeted inhibition and targeted degradation of the epidermal growth factor receptor (EGFR), one of the major proteins responsible for the onset and progression of many types of cancer. In addition, we develop an alternative strategy, called alloAUTO, based on the binding of new heterocyclic compounds to an allosteric site located in close proximity to the EGFR catalytic site. These compounds cause the targeted degradation of the transmembrane receptor, simultaneously activating both systems of protein degradation in cells. Damage to the EGFR signaling pathways promotes the inactivation of Bim sensor protein phosphorylation, which leads to the disintegration of the cytoskeleton, followed by the detachment of cancer cells from the extracellular matrix, and, ultimately, to cancer cell death. This hallmark of targeted cancer cell death suggests an advantage over other targeted protein degradation strategies, namely, the fewer cancer cells that survive mean fewer chemotherapy-resistant mutants appear.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10526213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41158122","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":"Benchmarking RNA Editing Detection Tools.","authors":"David Rodríguez Morales,&nbsp;Sarah Rennie,&nbsp;Shizuka Uchida","doi":"10.3390/biotech12030056","DOIUrl":"https://doi.org/10.3390/biotech12030056","url":null,"abstract":"<p><p>RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identified: (1) the most frequent, adenosine to inosine (A-to-I); and (2) the less frequent, cysteine to uracil (C-to-U) RNA editing. Unlike other epitranscriptomic marks, RNA editing can be readily detected from RNA sequencing (RNA-seq) data without any chemical conversions of RNA before sequencing library preparation. Furthermore, analyzing RNA editing patterns from transcriptomic data provides an additional layer of information about the epitranscriptome. As the significance of epitranscriptomics, particularly RNA editing, gains recognition in various fields of biology and medicine, there is a growing interest in detecting RNA editing sites (RES) by analyzing RNA-seq data. To cope with this increased interest, several bioinformatic tools are available. However, each tool has its advantages and disadvantages, which makes the choice of the most appropriate tool for bench scientists and clinicians difficult. Here, we have benchmarked bioinformatic tools to detect RES from RNA-seq data. We provide a comprehensive view of each tool and its performance using previously published RNA-seq data to suggest recommendations on the most appropriate for utilization in future studies.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"12 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10527054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41152521","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}