Electronic Journal of Biotechnology最新文献

Background

Cadmium (Cd²⁺) is one of the highly toxic heavy metals and is considered as a carcinogenic agent. Our aim was to confirm the ability of Frankia alni ACN14a to resist Cd²⁺ and to determine the genes involved in the resistance mechanism.

Results

F. alni ACN14a and Frankia casuarinae CcI3 hyphae showed up to 10 and 22 times Cd²⁺ accumulation when exposed to 1 mM Cd²⁺, respectively. Scanning electron microscopy (SEM) exhibited a stable Cd²⁺ precipitate on the cell surface, and the increase in Cd²⁺ weight level reached 16.45% when evaluated with SEM-EDAX analysis. The following two potential Cd²⁺ operons were identified: 1. cadCA operon, which encodes a copper-transporting P-type ATPase A (cadA, FRAAL0989) and an ArsR family regulator (cadC, FRAAL0988), with 37- and 70-fold increase in their expression by qRT-PCR, respectively and 2. cadB/DX, which encodes a putative cobalt-zinc-cadmium resistance protein (cadD, FRAAL3628) and heavy metal-associated domain protein (cadX, FRAAL3626), with 22- and 16-fold upregulation when exposed to Cd²⁺ stress.

Conclusions

Cd²⁺ tolerance by F. alni ACN14a involved efflux of Cd²⁺ outside the cells and binding it to the membrane surface. Our results indicate the existence of two cadmium-resistance mechanisms in Frankia strains, which support the idea of using them as a bioremediation agent.

How to cite: Rehan M, Alhusays A, Serag AM, et al. The cadCA and cadB/DX operons are possibly induced in cadmium resistance mechanism by Frankia alni ACN14a. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.006.

Background

Integrin subunit α -v (ITGAV) has been demonstrated to be dysregulated and involved in cancer promotion processes in a variety of cancers, but studies on nasopharyngeal carcinoma (NPC) have been limited. Our study aimed to comprehensively assess the expression level and potential mechanisms of ITGAV in NPC.

Results

A total of 13 mRNA expression datasets and internal tissue microarrays were included. ITGAV protein and mRNA were overexpressed in NPC. The pathways of upregulated genes positively related to ITGAV in NPC were analyzed, and the PI3K−Akt signaling pathway, cell cycle, and human papillomavirus infections were most significantly enriched. The protein–protein interaction network was constructed for the genes enriched in these pathways, and the corresponding hub genes were obtained. Among them, breast cancer susceptibility gene 1 (BRCA1) was predicted to be a transcription factor of ITGAV via the Cistrome DB Toolkit, which was also confirmed by ChIP-seq information and correlation calculations.

Conclusions

ITGAV is overexpressed in NPC and can regulate BRCA1 to participate in the cancer process. ITGAV serves as a potential therapeutic target in NPC patients.

How to cite: Huang S-W, Luo J-Y, Qin L-T, et al. Upregulation of ITGAV and the underlying mechanisms in nasopharyngeal carcinoma. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.002.

Background

Leucine zipper protein 2 (LUZP2) is a vital gene encoding leucine zipper protein. It is of great importance in the incidence and progress of several human cancers. However, little is known about the role and clinical effects of LUZP2 in prostate cancer (PCa). Therefore, it is crucial to unravel the clinicopathological value of LUZP2 in PCa. In all, 1467 PCa and 549 non-prostate cancer (non-PCa) prostate samples were collected from mRNA chip and RNA-sequencing datasets. The protein levels of LUZP2 were verified in 91 prostate gland tissues by in-house immunohistochemistry (IHC). The standardized mean difference (SMD) was calculated to analyze LUZP2 expression. Survival analysis was also conducted to explore the prognostic significance of LUZP2 in PCa. R software was employed to identify the upregulated differently expressed genes (up-DEGs) and coexpressed genes (CEGs) of LUZP2. Additionally, we explored the prospective molecular mechanism of CEGs of LUZP2 through GO and KEGG pathway analyses.

Results

Compared with non-PCa, LUZP2 showed predominantly higher expression in PCa (SMD = 1.05, AUC = 0.88). IHC indicated the protein expression level of LUZP2 was consistently upregulated in PCa tissues (SMD = 2.23, 95%CI: 1.67–2.79). LUZP2 upregulation had an AUC of 0.88 (95%CI: 0.85–0.90) to distinguish PCa from non-PCa tissues. KEGG pathway analysis showed that the pathways of amino sugar and nucleoside sugar metabolism were chiefly enriched with the LUZP2 CEGs in PCa.

Conclusion:

LUZP2 upregulation might play a promoting function in the occurrence of PCa.

How to cite: Li S-H, Yang Y-P, He R-Q, et al. Comprehensive expression analysis reveals upregulated LUZP2 in prostate cancer tissues. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.06.001

Background

Camels are known for their survival under harsh and nutrient-deficient climates. Camel rumen ecosystem presents a unique opportunity to study the ruminal microbes helping the camel in this task. The genus Aspergillus is the extensively studied filamentous fungus due to its ability to secret industrially important enzymes. The present study was aimed to isolate and characterize microbes with lignocellulolytic capacity from camel rumen.

Results

The fungal isolate Aspergillus sydowii C6d, isolated from camel rumen, was sequenced and analysed for its CAZyme content responsible for lignocellulose degradation. The C6d isolate was evaluated for its capacity to produce cellulase, pectinase, xylanase, and amylase with their respective assays and further evaluated for their optimum pH. The genome sequencing and assembly resulted in 32.27 Mb of genome size with a GC % of 50.59. The CAZyme analysis revealed that the C6d produced 543 polysaccharide-degrading CAZymes amongst which, 148 CAZymes were potentially involved in lignocellulose degradation. The genomic comparison of the C6d with 30 commonly used lignocellulolytic fungi (white rot, brown rot, and soft rot fungus) showed the enrichment of cellulolytic and pectinolytic CAZymes in C6d genome as compared to others. The saccharification of lignocellulosic substrate wheat straw resulted in the release of 50.85% of reducing sugars.

Conclusions

The study provides important insights into the CAZymes responsible for lignocellulolytic ability in the novel fungus Aspergillus sydowii C6d isolated from camel rumen and presents a valuable source of CAZymes to be further evaluated for potential biotechnological applications.

How to cite: Tulsani NJ, Jakhesara SJ, Hinsu AT, et al. Genome analysis and CAZy repertoire of a novel fungus Aspergillus sydowii C6d with lignocellulolytic ability isolated from camel rumen. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.06.004.

Background

Diverse plants respond differently to similar saline conditions. The aim of the current study was to determine the variation in the foliar contents of phenolic compounds, carotenoids, and proline, and the variation of the activities of catalase (CAT) and superoxide dismutase (SOD) of the edible and medicinal Physalis ixocarpa throughout three different times of exposure (24, 42, and 57 d) to three salinity levels (0, 90, and 120 mM NaCl). The specific effects of salt concentration and time of exposure were also assessed.

Results

Proline increase was the only clearly salt-related response, evidencing its significant protective role in salinized P. ixocarpa under either short, medium, or chronic exposure. One phenolic acid, which increased up to 26.26 times its concentration (compared to control, under high salinity at the longest treatment) out of the eight compounds forming the phenolic profile of the species, and CAT and SOD, under 90 and 120 mM NaCl, respectively, and short and medium exposure, also made important contributions. Salt concentration mainly affected total phenolics, tannins, phenolic acids (PA), proline, and SOD, whereas exposure time mainly affected flavonoids, carotenoids, and CAT.

Conclusions

The participation of the different protection mechanisms of P. ixocarpa against salinity is dynamic and complementary, and it is differentially modulated by the salt concentration and the time of exposure. Proline is the main mechanism for the species. The accurate chronic registration of the responses is needed to determine its adaptation potential to salt stress. The results have agronomic and food quality implications.

How to cite: Hernández-Pacheco CE, Almaraz-Abarca N, Marlon Rojas-López M, et al. Salinity generates varying chemical and biochemical responses in Physalis ixocarpa (Solanaceae) during different times of exposure. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.06.002

Background

Protected agriculture (PA) is an alternative allowing the control of environmental variables to produce healthy vegetables. Biofertilizers and biofungicides can reduce the chemical load of pesticides. There is abundant literature documenting individual aspects, such as control of environmental variables, irrigation, biological control, and cost assessments. However, there are no reports documenting integral approaches in which variables are considered altogether in a successful case study of mid-tech technology, suitable in middle-income countries like México. We tested if mid-tech greenhouses using biocontrol and biofertilization can increase profits, using tomato as a model system. This work provides considerations about middle-income countries’ agriculture and the need for a multidisciplinary approach to offer cost-effective, sustainable alternatives to producers.

Results

This technology yielded up to 254 tons/ha·year of tomato, achieving reductions of 44–60% in water consumption, 25% in chemical nitrogen-fertilization, and 28% in the cost unit of production, increasing the profits by ∼45% in relation to Mexican conventional greenhouses management.

Conclusions

This case study has shown that it is possible to significantly increase profits in mid-tech greenhouse tomato production by increasing productivity and crop quality and decreasing the use of water and agrochemicals through greenhouse automatization, crop management, and beneficial bacteria applied to crops. This manuscript includes a video, supplementary to the main contributions of the project. Please visit this URL: https://youtu.be/uRBGgJqfkLE.

How to cite: Serrano-Carreón L, Aranda-Ocampo S, Balderas-Ruíz KA, et al. A case study of a profitable mid-tech greenhouse for the sustainable production of tomato, using a biofertilizer and a biofungicide. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.06.003.

Background

Bacterial cells often harbor multiple plasmids, but the interaction between these plasmids is poorly understood. Pseudomonas putida ND6, one of the typical naphthalene-degrading bacteria, contains two annotated plasmids, pND6-1 and pND6-2. The conjugative plasmid pND6-2 can be used as a helper to mobilize the naphthalene-degrading plasmid pND6-1. The role of pND6-1 in functions other than naphthalene degradation has never been explored. Therefore, it is of great significance to study the possible effect of pND6-1 on the transfer rate or maintenance of pND6-2.

Results

To investigate the interaction between pND6-1 and pND6-2, we successfully cured plasmid pND6-1 using the incompatibility method, generated the pND6-1-null strain ND6dp1, and first classified it into the IncP-7 group by curing experimental evidence. Subsequently, the pND6-1-cured mutant showed an insignificant increase in cell growth compared with the wild ND6, indicating that a lower cost was imposed on the host by pND6-1. The influences of pND6-1 on the stability and conjugation of plasmid pND6-2 were subsequently explored. The results showed that the presence of pND6-1 enhanced the stability of pND6-2 in natural host ND6 and heterologous host P. putida KT2440. In addition, the presence of pND6-1 in wild-type hosts promoted intra-specific and inter-specific conjugative transfer efficiency of pND6-2 by 3.9–6.3-fold with P. putida, P. resinovans, and P. fluorescens as the recipients, respectively.

Conclusions

Collectively, these results suggest that the plasmid pND6-1 improves the pND6-2 plasmid's stability and transfer rate in the ND6 strain with the selected recipient strains.

How to cite: Wang S, Liu M, Wang D, et al. Plasmid pND6-1 enhances the stability and conjugative transfer of co-resident companion plasmid pND6-2 in the naphthalene-degradative Pseudomonas putida strain ND6. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.08.002.

Background

Endosomally produced by eukaryotic cells, exosomes are microvesicles involved in cell-to-cell communication. Exosomes have shown a wide range of therapeutic potential as a drug or vaccine delivery system, and they are useful as biomarkers in several disease processes. Another biological function described is pathogen dissemination through host-derived molecules released during infection, thus modulating the immune response in the host.

Results

This work characterizes the exosomal fraction recovered from serum of Piscirickttesia salmonis-challenged Salmo salar specimens and from the corresponding non-challenged controls. Exosomes presented a spherical morphology and particle size distribution within 50–125 nm, showing similar parameters in both groups. The mass spectrometry analysis of exosomes isolated at 14 and 21 d post-challenge showed the presence of peptides corresponding to the three proteins of Hsp70/DnaK chaperone system (DnaK, DnaJ, and GrpE). BLAST search of these peptides showed the specificity to P. salmonis. Data are available via ProteomeXchange with identifier PXD023594.

Conclusions

The chaperones were found with >95% identity in the core genome when aligned to 73 genomes of P. salmonis. The proteins also showed a high degree of similarity with other microorganisms, where this system has proven to be vital for their survival under stress conditions.

The presence of these three proteins in exosomes isolated from challenged fish sera calls for further study into their potential role in bacterium pathogenicity.

How to cite: Muñoz C, Carmona M, Luna O, et al. Serum-isolated exosomes from Piscirickettsia salmonis-infected Salmo salar specimens enclose bacterial DnaK, DnaJ and GrpE chaperones. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.07.003.

Background

The temperature upshift has been widely used as an induction system to produce recombinant proteins (RPs). However, thermoinduction could affect bacterial metabolism, RP production, and RP aggregation. Understanding the structure and functionality of those aggregates, known as inclusion bodies (IBs), is a research area of interest in bioprocesses being scarcely studied under thermoinduction. Here, we describe the effect of the thermoinduction (39°C or 42°C) on the production of the recombinant human granulocyte–macrophage colony-stimulating factor (rHuGM-CSF) using Escherichia coli W3110 under the system λpL/cI857.

Results

Results indicated that at 39°C, the production of biomass was almost doubled as well as the acetate accumulation compared to 42°C. Cultures thermoinduced at 42°C improved 1.5-fold the total protein over biomass yield and 1.25-fold the RP over total protein yield. Furthermore, 42°C accelerated the onset of IB formation, changing its architecture. Additionally, IBs formed at 42°C were less soluble and presented higher disorderly structures compared with IBs formed at 39°C, enriched in α-helix and amyloidal-like structures.

Conclusions

This study highlights the observation that IBs attain different architecture in response to small changes in environmental conditions, such as the induction temperature, being this helpful information to improve thermoinduced bioprocesses.

How to cite: Restrepo-Pineda S, Rosiles-Becerril D, Vargas-Castillo AB, et al. Induction temperature impacts the structure of recombinant HuGM-CSF inclusion bodies in thermoinducible E. coli. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.08.004.

Background

Hair follicle development is important for the fineness of wool. Our previous methylated DNA immunoprecipitation sequencing showed that IGFBP2 and IGFBP4 were differentially methylated at different development stages of the hair follicle of Super Merino sheep. This study selected these two genes as candidates to uncover the influence of their promoter methylation on hair follicle development.

Results

The results showed that the expression levels of IGFBP2 and IGFBP4 in the skin of very fine wool Super Merino sheep were higher than that in the very thick wool group, and the difference for IGFBP4 was significant. The total methylation rate of IGFBP2 promoter was extremely low, and no significant difference was found in the skin tissue of the Super Merino sheep at different fineness groups. However, the total methylation rate of IGFBP4 promoter in the very thick group was significantly higher than that in the very fine group, and the total DNA methylation levels of the IGFBP4 were significantly negatively correlated with mRNA expression. Furthermore, the transcription factor prediction results showed 104 and 91 candidate binding sites for transcription factors in the promoter regions of IGFBP2 and IGFBP4, respectively. Among these, JUN, EP300, SP1, PAX6, ETS1, and MYOD1 may be related to hair follicle development.

Conclusions

The total methylation level of IGFBP4 promoter was negatively correlated with its mRNA expression in Super Merino sheep skin tissues with different degrees of fineness, which could be used as an epigenetic marker for wool breeding in Super Merino sheep.

How to cite: Tian Y, Du J, Yang X, et al. Sheep IGFBP2 and IGFBP4 promoter methylation regulates gene expression and hair follicle development. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.07.001.