• Animal Bioscience
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• 제37권4호
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• pp.655-667
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• 2024

Objective: This study aimed to assess the impact of a hydroethanolic extract of walnut green husks (WGH) on rumen fermentation and the diversity of bacteria, methanogenic archaea, and fungi in sheep fed a high-concentrate diet. Methods: Five healthy small-tailed Han ewes with permanent rumen fistula were selected and housed in individual pens. This study adopted a self-controlled and crossover design with a control period and an experimental period. During the control period, the animals were fed a basal diet (with a ratio of concentrate to roughage of 65:35), while during the treatment period, the animals were fed the basal diet supplemented with 0.5% hydroethanolic extract of WGH. Fermentation parameters, digestive enzyme activities, and microbial diversity in rumen fluid were analyzed. Results: Supplementation of hydroethanolic extract of WGH had no significant effect on feed intake, concentrations of total volatile fatty acids, isovalerate, ammonia nitrogen, and microbial protein (p>0.05). However, the ruminal pH, concentrations of acetate, butyrate and isobutyrate, the ratio of acetate to propionate, protozoa count, and the activities of filter paper cellulase and cellobiase were significantly increased (p<0.05), while concentrations of propionate and valerate were significantly decreased (p<0.05). Moreover, 16S rRNA gene sequencing revealed that the relative abundance of rumen bacteria Christensenellaceae R7 group, Saccharofermentans, and Ruminococcaceae NK4A214 group were significantly increased, while Ruminococcus gauvreauii group, Prevotella 7 were significantly decreased (p<0.05). The relative abundance of the fungus Pseudomonas significantly increased, while Basidiomycota, Fusarium, and Alternaria significantly decreased (p<0.05). However, there was no significant change in the community structure of methanogenic archaea. Conclusion: Supplementation of hydroethanolic extract of WGH to a high-concentrate diet improved the ruminal fermentation, altered the structure of ruminal bacterial and fungal communities, and exhibited beneficial effects in alleviating subacute rumen acidosis of sheep.

• Journal of Microbiology and Biotechnology
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• 제11권4호
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• pp.709-711
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• 2001

To elucidate the putative role of the amido group in the metal binding of the fuculose-1-phosphate aldolase from Methanococcus jannaschii, we have examined a potential targen using site-directed mutagenesis. The replacement of asparagine 25 with leucine or threonine was shown to have a negative effect, not only on catlytic efficiency, but also on substrage recognition as well. The Hill coefficient values yeilded a value of =1. All metals used with the wild-type aldolases exhibited higher activity than that of the mutants. The spectra of the mutants were quite different from the wild-type aldolase. A highly conserved amino acid of asparagine 25 in a related family of aldolase odes not appear to provide sufficient evidence for evolution.

• Biotechnology and Bioprocess Engineering:BBE
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• 제3권2호
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• pp.115-118
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• 1998

Utilization of yeast extract and formation of byproduct metabolite were investigated for hyperthermophilic archaeon Sulfolobus solfataricus (DSH 1617). In both batch and fed-batch cultivations of S. solfataricus, maximal cell density, {{{{ { NH}`_{4 } ^{ +} }}} ion production and pH change were highly dependent on the ratio of yeast extract to glucose in the medium. Variation of {{{{ { NH}`_{4 } ^{ +} }}}} ion level was identified as a major cause of pH change during cultivation, and acidification of culture broth was attributed to consumption of {{{{ { NH}`_{4 } ^{ +} }}}} ions rather than formation of acid byproducts. It was also observed that increase of {{{{ { NH}`_{4 } ^{ +} }}}} ion concentrations in the medium resulted in greater degree of growth inhibition.

• Genomics & Informatics
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• 제15권1호
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• pp.38-47
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• 2017

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

• Journal of Microbiology
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• 제39권4호
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• pp.254-264
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• 2001

Sponges are host organisms for various symbiotic microorganisms such as archaea, bacteria, cyano-bacteria and microalgae. Sponges are also sources of a wide variety of useful natural products like cyto-toxins. antifouling agents, antibiotics, and anti-inflammatory and antiviral compounds, Symbiotic microorganisms is sponges can be sources of various natural products, because metabolites previously ascribed to sponges have recently been demonstrated to be biosynthesized by symbionts. If a symbiotic microorganisms from which some natural products are derived can be cultured, the microorganism could be used in a mass production of the bioactive comopounds. We summarize recent research on iso-lation and cultivation of sponge-symbiotic microorganisms and the symbiotic relationship.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2000년도 Proceedings of 2000 KSAM International Symposium and Spring Meeting
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• pp.135-141
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• 2000

Global Biodiversity is common interest of humans for better health and sustainable development of the society. To provide access and analysis on microbial diversity information, Bacteriology Insight Orienting System (BIOS) has been developed. BIOS contains 6402 species and subspecies names of bacteria and archaea, 2606 names of cyanobacteria by March 2000. BIOS of which web based analytical tool provides windows to compare the results of phylogenetic analysis based on 16S rDNA sequence and the results of cluster analysis on proteome profiling. The sequence data and 2 dimensional gel electrophoresis analysis data were accumulated in BIOS database content for cyanobacteria reclassification and taxonomy. (BIOS URL: http.://www-sp2000ao.nies.go.jp/bios/index.html).

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1996년도 정기총회 및 학술발표회
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• pp.30-30
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• 1996

A suproxide dismutase gene of Aquifex pyroprolus, a novel marine hypenhermophilic bacterium, was cloned, expressed, and characterized. The SOD of A pyrophilus (ApSOD) is an iron-containing homo-oligomeric protein with a monomeric molecular weight of 24.2 kDa. the amino acid sequence is similar to those of known Mn- and Fe-SODs from thermophilic archaea, and metal binding residues in all SOD sequences from different species are also conserved in A. pyrophilus SOD. (omitted)

• Genomics & Informatics
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• 제7권1호
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• pp.26-31
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• 2009

Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria. This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.

• 한국자기공명학회논문지
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• 제25권3호
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• pp.39-44
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• 2021

The CRISPR-Cas system provides adaptive immunity for bacteria and archaea against invading phages and foreign plasmids. In the Class 1 CRISPR-Cas system, multi-subunit Cas proteins assemble with crRNA to bind to DNA targets. To disarm the bacterial defense system, bacteriophages evolved anti-CRISPR (Acr) proteins that actively inhibit the host CRISPR-Cas function. Here we report the backbone resonance assignments of AcrIF7 protein that inhibits the type I-F CRISPR-Cas system of Pseudomonas aeruginosa using triple-resonance nuclear magnetic resonance spectroscopy. We employed various computational methods to predict the structure and binding interface of AcrIF7, and assessed the model with experimental data. AcrIF7 binds to Cas8f protein via flexible loop regions to inhibit target DNA binding, suggesting that conformational heterogeneity is important for the Cas-Acr interaction.

• Journal of Microbiology and Biotechnology
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• 제31권7호
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• pp.903-911
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• 2021

Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.