Hasil untuk "Biotechnology"

L. Pierson, E. Pierson

Phenazines constitute a large group of nitrogen-containing heterocyclic compounds produced by a diverse range of bacteria. Both natural and synthetic phenazine derivatives are studied due their impacts on bacterial interactions and biotechnological processes. Phenazines serve as electron shuttles to alternate terminal acceptors, modify cellular redox states, act as cell signals that regulate patterns of gene expression, contribute to biofilm formation and architecture, and enhance bacterial survival. Phenazines have diverse effects on eukaryotic hosts and host tissues, including the modification of multiple host cellular responses. In plants, phenazines also may influence growth and elicit induced systemic resistance. Here, we discuss emerging evidence that phenazines play multiple roles for the producing organism and contribute to their behavior and ecological fitness.

Shuangshuang Wan, Yu Lei, Yue Jin et al.

Abstract The incidence of Clostridioides difficile infection (CDI) has been rising globally in recent years. Treating CDI is complicated by antibiotic-induced disruption of the normal gut microbiota, which promotes CDI recurrence and increases the risk of therapeutic failure. We used an AI-assisted approach to screen small molecule inhibitors targeting the receptor binding domain of toxin B (TcdB). Biliverdin (BV) had strong binding affinities with all TcdB variants. In vitro results showed that BV exhibited no cytotoxic effects on cells and didn’t affect growth of C. difficile, yet markedly suppressed cytotoxic effects induced by TcdB1-4. Encapsulating BV in intestinal epithelial cell-derived extracellular vesicles (I-EVs) significantly recovered body weight, enhanced survival rate, reduced TcdB load, and alleviated intestinal lesions in treated gerbils. Notably, BV treatment not only restored the abundance of gut microbiota but also significantly increased the quantity of gut-beneficial Firmicutes. BV also exerted its anti-CDI effect by restoring the short-chain fatty acid metabolic network. Our findings indicate that BV shows promise as a natural small-molecule therapeutic that attenuates broad-spectrum TcdB-induced injuries, highlighting its potential for clinical translation in CDI treatment.

Utpal Jyoti Das, Deepjyoti Mali

The current study contains a steady laminar bioconvective magnetohydrodynamic (MHD) flow involving water (H2O)-based hybrid nanofluid composed of silver (Ag) and alumina oxide (Al2O3) as nanoparticles. This flow passes over a thin moving slender needle including gyrotactic motile microorganisms through a porous medium. The study examines how various physical characteristics, such as Cattaneo-Christov heat and mass flow, and viscous dissipation, affect the system's flow. Our objective is to find the impact of pertinent parameters on velocity, temperature, concentration, and microorganisms. This type of flow problem is important to control the heat and fluid flow phenomena around a needle which are applied to biotechnology (bioreactors, microbial fuel cells), biomedical engineering, microfluidics, and cooling systems. The reason for this investigation combines both scientific curiosity and practical applications. The controlling equations are simplified into nonlinear ordinary differential equations, solved numerically via MATLAB bvp4c tool, and their impact on temperature, velocity, microorganism, and concentration outline is graphically depicted, also, their impact on local microorganism's number, local Sherwood number, frictional drag coefficient, and local Nusselt number, are tabulated. This study's novelty is that it fills the gaps left by Kandasamy et al. [31]. This study demonstrates great agreement with Kandasamy et al. [31]. The study's findings indicate that improvement of thermal and concentration relaxation parameters declines fluid temperature and concentration respectively. Also, enhancement of bioconvection Lewis and Peclet numbers diminishes the microorganisms' profile. Again, when the Dufour and Soret numbers rise, then the temperature and concentration distribution also improve respectively. Furthermore, introducing 1 % of alumina oxide (Al2O3), and silver (Ag) nanoparticles into the base fluid increased frictional drag by 2.64 %, and 3.03 %, respectively, compared to water.

Weitong Yao, Yujun Li, Huize Sun et al.

IntroductionThe beta-coronavirus SARS-CoV-2 has been revealed to infect mammals and other species, which potentially promotes the virus adaptation to broader species and the emergence of new variants. The host range of different SARS-CoV-2 variants are mainly determined by the affinity of the receptor-binding domain (RBD) of the spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Thus, this study aims to elucidate the detailed mechanisms of such dynamic adaptation of indicated SARS-CoV-2 variants.MethodsIn this study, flow cytometry and surface plasmon resonance (SPR) assays were used to assess the binding affinity between RBDs and avian ACE2. Then, infection assays with MLV-based SARS-CoV-2 spike pseudovirus or authentic viruses were performed to verify the avian ACE2 mediated viral entry. Finally, mutagenesis studies were conducted to identify key amino acids of avian ACE2 orthologs and RBDs.ResultsOur previous findings revealed that wild-type SARS-CoV-2 RBD does not bind chicken ACE2. Here, we found that ACE2 orthologs from chicken and mallard were capable to support binding to RBDs of the Alpha, Beta, and Gamma variants, which further enabled the viral entry. On the contrary, the RBD of BA.1 failed to bind avian ACE2. Whereas, a triple-residue reversal mutant (S446G, S496G, H505Y) restored ACE2 binding and enabled efficient viral entry. Additionally, several key residues within RBD were characterized as the determinant of its affinity to avian ACE2.DiscussionOur findings reveal that higher mutation rates in emerging variants might lead to future cross-species receptor usage or even spillover. Understanding such cross-species transmission mechanisms provides new insights to the virological features and potential host range of emerging SARS-CoV-2 variants.

Maher Alnajjar, Zsófia Fekete, Tibor Nagy et al.

Allele-specific expression (ASE) reflects the unequal expression of the parental alleles and can imply functional variants in cis-regulatory elements. The conventional ASE detection methods often depend on the presence of heterozygous variants in transcripts or sequencing a large number of individuals, both of which are often limited. In this study, we present a family-based strategy for detecting ASE and potential cis-regulatory elements utilizing both RNA-seq and whole-genome sequencing (WGS) from a pedigree. Using a rabbit family consisting of two divergent parents and their eight offspring, we identified 913 ASE genes by analyzing inheritance patterns of gene expression levels. Expression was classified into three levels—high, medium, and low—and used to define seven distinct expression groups across the family (e.g., H_L: high in the mother, low in the father, and intermediate in the offspring). Many ASE genes lacked heterozygous exonic variants, and inference was achieved via RNA read count patterns. We also pinpointed conserved transcription factor binding sites (TFBS) with sequence variants showing similar inherited genotypic patterns (e.g., AAxBB), suggesting their regulatory roles as eQTLs. Differential gene expression (DEG) analysis between the parents highlighted some candidate genes related to meat production and quality traits. Our findings show that the family-based method using RNA-seq and WGS data is promising for exploring ASE and mapping possible eQTLs.

Xin Li, Xiaoqian Wang, C. Duan et al.

Although biotechnologies for astaxanthin production from Haematococcus pluvialis have been developed for decades and many production facilities have been established throughout the world, the production cost is still high. This paper is to evaluate the current production processes and production facilities, to analyze the R&D strategies for process improvement, and to review the recent research advances shedding light on production cost reduction. With these efforts being made, we intent to conclude that the production cost of astaxanthin from Haematococcus might be substantially reduced to the levels comparable to that of chemical astaxanthin through further R&D and the future research might need to focus on strain selection and improvement, cultivation process optimization, innovation of cultivation methodologies, and revolution of extraction technologies.

M. Bilal, M. Asgher, Hairong Cheng et al.

Abstract Engineering enzymes with improved catalytic properties in non-natural environments have been concerned with their diverse industrial and biotechnological applications. Immobilization represents a promising but straightforward route, and immobilized biocatalysts often display higher activities and stabilities compared to free enzymes. Owing to their unique physicochemical characteristics, including the high-specific surface area, exceptional chemical, electrical, and mechanical properties, efficient enzyme loading, and multivalent functionalization, nano-based materials are postulated as suitable carriers for biomolecules or enzyme immobilization. Enzymes immobilized on nanomaterial-based supports are more robust, stable, and recoverable than their pristine counterparts, and are even used for continuous catalytic processes. Furthermore, the unique intrinsic properties of nanomaterials, particularly nanoparticles, also confer the immobilized enzymes to be used for their broader applications. Herein, an effort has been made to present novel potentialities of multi-point enzyme immobilization in the current biotechnological sector. Various nano-based platforms for enzyme/biomolecule immobilization are discussed in the second part of the review. In summary, recent developments in the use of nanomaterials as new carriers to construct robust nano-biocatalytic systems are reviewed, and future trends are pointed out in this article.

G. Gregoriadis

Yu-Jin Kim, Dabing Zhang, Deok-Chun Yang

R. Sheldon

Cross-linked enzyme aggregates (CLEAs) have many economic and environmental benefits in the context of industrial biocatalysis. They are easily prepared from crude enzyme extracts, and the costs of (often expensive) carriers are circumvented. They generally exhibit improved storage and operational stability towards denaturation by heat, organic solvents, and autoproteolysis and are stable towards leaching in aqueous media. Furthermore, they have high catalyst productivities (kilograms product per kilogram biocatalyst) and are easy to recover and recycle. Yet another advantage derives from the possibility to co-immobilize two or more enzymes to provide CLEAs that are capable of catalyzing multiple biotransformations, independently or in sequence as catalytic cascade processes.

K. Schutter, Yao-cheng Lin, P. Tiels et al.

The methylotrophic yeast Pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. P. pastoris strains capable of human-type N-glycosylation are now available, which increases the utility of this organism for biopharmaceutical production. Despite its biotechnological importance, relatively few genetic tools or engineered strains have been generated for P. pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes.

Nguyen Dinh-Hung, Samuel Mwakisha Mwamburi, Ha Thanh Dong et al.

This study aims to genomically elucidate six isolates of rapidly growing non-tuberculous mycobacteria (RGM) derived from Siamese fighting fish (<i>Betta splendens</i>). These isolates had previously undergone phenotypic and biochemical characterization, antibiotic susceptibility testing, and in vivo virulence assessment. Initial DNA barcoding using the 16S rRNA sequence assigned these six isolates to five different species, namely <i>Mycobacterium chelonae</i> (BN1983), <i>M. cosmeticum</i> (BN1984 and N041), <i>M. farcinogenes</i> (SNSK5), <i>M. mucogenicum</i> (BN1956), and <i>M. senegalense</i> (BN1985). However, the identification relied solely on the highest percent identity of the 16S rRNA gene, raising concerns about the taxonomic ambiguity of these species. Comprehensive whole genome sequencing (WGS) and extended genomic comparisons using multilocus sequence typing (MLST), average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH) led to the reclassification of BN1985 and SNSK5 as <i>M. conceptionense</i> while confirming BN1983 as <i>M. chelonae</i> and BN1984 and N041 as <i>M. cosmeticum</i>. Notably, the analysis of the BN1956 isolate revealed a potential new species that is proposed here as <i>M. mucogenicum</i> subsp. <i>phocaicum</i> sp. nov. Common genes encoding “mycobacterial” virulence proteins, such as PE and PPE family proteins, MCE, and YrbE proteins, were detected in all six isolates. Two species, namely <i>M. chelonae</i> and <i>M. cosmeticum</i>, appear to have horizontally acquired T6SS-II (<i>clpB</i>), catalase (<i>katA</i>), GroEL (<i>groel</i>), and capsule (<i>rmlb</i>) from distantly related environmental bacteria such as <i>Klebsiella</i> sp., <i>Neisseria</i> sp., <i>Clostridium</i> sp., and <i>Streptococcus</i> sp. This study provides the first draft genome sequence of RGM isolates currently circulating in <i>B. splendens</i> and underscores the necessity of WGS for the identification and classification of mycobacterial species.

Bekzhan Faizov, Alizhan Bukayev, Zhaxylyk Sabitov et al.

This study presents a comprehensive analysis of 23 Y-STR data for the Merkit clan, a subgroup within the Kerey tribe of the Kazakh people. A total of 64 complete haplotypes were generated using the PowerPlex Y23 System. The data obtained using 23 Y-STR markers has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) at yhrd.org, which will significantly enhance the forensic database for the Kazakh population in Kazakhstan. The research focuses on the distribution of haplotypes within the clan and their genealogical lines, which were visualized using a Median-joining network and Multidimensional scaling plot. The study identifies four distinct haplogroup clusters, revealing important insights into the genetic makeup and historical lineage of the Merkits. This dataset not only enriches our understanding of Kazakh genetic structure but also holds significant value for anthropological and population genetic research, as well as for forensic genetics. This work bridges a notable gap in genetic research on the Merkit clan, contributing to a deeper understanding of Central Asian nomadic tribes.

Haeun Kwon, Bo-Ram Jin, Hyo-Jung Kim et al.

Xiujuan Qian, Lin Chen, Y. Sui et al.

Recent advances in microbial consortia present a valuable approach for expanding the scope of metabolic engineering. Systems biology enable thorough understanding of diverse physiological processes of cells and their interactions, which in turn offers insights into the optimal design of synthetic microbial consortia. Yet, the study of synthetic microbial consortia is still in early infancy, facing many unknowns and challenges in intercellular communication and construction of stable and controllable microbial consortia systems. In this review, we comprehensively discussed the recent application of defined microbial consortia in the fields of human health monitoring and medicine exploitation, valuable compounds synthesis, consolidated bioprocessing of lignocellulosic materials and environmental bioremediation. Moreover, the outstanding challenges and future directions to advance the development of high-efficient, stable and controllable synthetic microbial consortia were highlighted.

G. Fonseca, E. Heinzle, C. Wittmann et al.

P. Schloss, J. Handelsman

Eliza Depoorter, M. Bull, Charlotte Peeters et al.

Xiaoyu Fu, Da Cheng, Zhenwu Luo et al.

Abstract Background . Up to 20% of people with HIV (PWH) who undergo virologically suppressed antiretroviral therapy (ART) fail to experience complete immune restoration. We recently reported that plasma anti-CD4 IgG (antiCD4IgG) autoantibodies from immune non-responders specifically deplete CD4 + T cells via antibody-dependent cytotoxicity. However, the mechanism of antiCD4IgG production remains unclear. Methods . Blood samples were collected from 16 healthy individuals and 25 PWH on suppressive ART. IgG subclass, plasma lipopolysaccharide (LPS), and antiCD4IgG levels were measured by ELISA. Gene profiles in B cells were analyzed by microarray and quantitative PCR. Furthermore, a patient-derived antiCD4IgG–producing B cell line was generated and stimulated with LPS in vitro. B cell IgG class switch recombination (CSR) was evaluated in response to LPS in splenic B cells from C57/B6 mice in vitro. Results . Increased plasma anti-CD4 IgGs in PWH were predominantly IgG1 and associated with increased plasma LPS levels as well as B cell expression of TLR2, TLR4, and MyD88 mRNA in vivo. Furthermore, LPS stimulation induced antiCD4IgG production in the antiCD4IgG B cell line in vitro. Finally, LPS promoted CSR in vitro. Conclusion . Our findings suggest that persistent LPS translocation may promote anti-CD4 autoreactive B cell activation and antiCD4IgG production in PWH on ART, which may contribute to gradual CD4 + T cell depletion. This study suggests that reversing a compromised mucosal barrier could improve ART outcomes in PWH who fail to experience complete immune restoration.

Md. Khirul Islam, Misba Khan, Kamlesh Gidwani et al.

Abstract Extracellular vesicles (EVs) have considerable potential as diagnostic, prognostic, and therapeutic agents, in large part because molecular patterns on the EV surface betray the cell of origin and may also be used to “target” EVs to specific cells. Cancer is associated with alterations to cellular and EV glycosylation patterns, and the surface of EVs is enriched with glycan moieties. Glycoconjugates of EVs play versatile roles in cancer including modulating immune response, affecting tumor cell behavior and site of metastasis and as such, paving the way for the development of innovative diagnostic tools and novel therapies. Entities that recognize specific glycans, such as lectins, may thus be powerful tools to discover and detect novel cancer biomarkers. Indeed, the past decade has seen a constant increase in the number of published articles on lectin-based strategies for the detection of EV glycans. This review explores the roles of EV glycosylation in cancer and cancer-related applications. Furthermore, this review summarizes the potential of lectins and lectin-based methods for screening, targeting, separation, and possible identification of improved biomarkers from the surface of EVs.