For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition ...data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.
There has been particular interest in the prebiotic-like effects of commonly consumed polyphenols. This study aimed to evaluate the effects of hesperidin (HD) and its aglycone hesperetin (HT), major ...flavonoids in citrus fruits, on the structure and activity of gut microbiota in rats. Rats ingested an assigned diet (a control diet, a 0.5% HT diet, or a 1.0% HD diet) for 3 weeks. Terminal restriction fragment length polymorphism analysis revealed that the proportion of Clostridium subcluster XIVa in the feces collected at the third week of feeding was significantly reduced by the HT diet: 19.8 ± 4.3% for the control diet versus 5.3 ± 1.5% for the HT diet (P < 0.01). There was a significant difference in the cecal pool of short-chain fatty acids (SCFA), the sum of acetic, propionic, and butyric acids, between the control diet (212 ± 71 μmol) and the HT diet (310 ± 51 μmol) (P < 0.05), whereas the HD diet exhibited no effects (245 ± 51 μmol). Interestingly, dietary HT resulted in a significant increase in the excretion of starch in the feces. HT, but not HD, might reduce starch digestion, and parts of undigested starch were utilized to produce SCFA by microbial fermentation in the large intestine.
An asymmetric total synthesis of lycopoclavamine-A (1), a structurally unique fawcettimine-type Lycopodium alkaloid, was achieved via a stereoselective Pauson–Khand reaction and a stereoselective ...conjugate addition to construct a quaternary carbon center at C-12.
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular ...mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
Quercetin is a polyphenol found in food that has numerous health benefits. This study investigated the relationship between quercetin metabolism, gut microbiota composition, and dietary intake in ...elderly Japanese subjects. A food frequency questionnaire was used to assess dietary intake during the week prior to stool sample collection. Fecal suspensions from 56 subjects were anaerobically incubated with quercetin and fecal microbiota composition was analyzed by next-generation sequencing. Inter-individual variations in quercetin concentration and fecal microbiota composition at family level suggested differences in microbial quercetin metabolism. The abundance of Sutterellaceae (r = -0.292) and Oscillospiraceae (r = -0.334) was negatively correlated whereas that of Fusobacteriaceae (r = 0.361) and Enterobacteriaceae (r = 0.321) was positively correlated with quercetin concentration. Niacin (r = -0.313), vitamin B6 (r = -0.297), vitamin B12 (r = -0.266), vitamin D (r = -0.301), and ratio of animal protein to total protein (r = -0.27) were also negatively correlated with quercetin concentration. Bacterial abundance was positively or negatively related to intake of food components. This is the first report describing the relationship between fecal quercetin metabolism, human microbiota, and dietary intake in the elderly.
•Production of yeast-expressed wheat lipoxygenase isozyme III (LOX III) and Nterminal truncated LOX III isozyme (Mini-LOX III) was established.•Wheat recombinant LOX III and Mini-LOX III extracted ...from yeast acted as linoleic acid substrates.•The polypeptide composition of soluble glutenin was changed by adding wheat recombinant LOX III or Mini-LOX III.
This study investigated the effects of wheat lipoxygenase isozyme III (LOX III) and its truncated form, Mini-LOX III, on flour dough properties using yeast-expressed recombinant enzymes and hypothesized their potential to enhance cereal-based food quality. These enzymes actively catalyze linoleic acid, which is crucial for dough formation. The addition of recombinant LOX III and Mini-LOX III to wheat flour significantly changed glutenin protein composition. An increase in the amount of soluble glutenin and a shift in polypeptide distribution were observed, marked by a decrease in the high-molecular-weight regions and an increase in the low-molecular-weight regions. This result reflects the role of enzymes in altering the hydrophobicity of glutenin surfaces, thereby affecting the protein solubility and dough properties. Thus, recombinant LOX III and Mini-LOX III offer new avenues for enhancing the texture and quality of cereal-based foods, providing valuable insights into the role of wheat LOX in flour processing and its potential industrial applications.
We propose off-axis virtual-image display and camera systems, which integrate a vertically-standing holographic off-axis mirror, blur-compensation optical systems, and digital imaging devices. In the ...system, the holographic mirror is used for an off-axis reflector, which realizes an upright and thin screen for virtual-image formation. By combining it with a display unit, an off-axis virtual-image display is realized, where the virtual image can be seen behind the upright holographic mirror. Simultaneously, by combining it with a camera unit, an off-axis camera is implemented, which realizes frontal shooting of objects by a camera placed at an off-axis position. Since both the off-axis display and the camera can be implemented by a single holographic mirror, it can be applied to a two-way visual-telecommunication system with a thin screen, which implements eye contact and the observer--image distance. A problem with the proposed system is image blur, which is caused by the chromatic dispersion of the holographic mirror. To solve this, we designed optical blur-compensation systems using a diffractive optical element and a diffuser or a lens. Experimental results verify the concept of the proposed systems with clarifying the effect of designed blur-compensation methods.
Activin A, a member of the transforming growth factor-beta superfamily, is a critical modulator of inflammation and plays a key role in controlling the cytokine cascade that drives the inflammatory ...response. However, the role of activin A in inflammatory kidney diseases remains unknown. To address this issue, we examined here whether activin A can be detected in the kidney and/or urine from patients with antineutrophil cytoplasmic antibody (ANCA) -associated vasculitis (AAV). Fifty-one patients who had been diagnosed with AAV and were treated in our department between November 2011 to March 2018 were included in this study. Forty-one patients had renal complications (renal AAV). Serum and urinary activin A levels were measured by enzyme-linked immunosorbent assay. Correlation of urinary activin A concentration with clinical parameters was analyzed. Urinary activin A was undetectable in healthy volunteers. In contrast, urinary activin A concentration was significantly increased in patients with renal AAV but not in those with non-renal AAV. Urinary activin A concentration decreased rapidly after immunosuppressive treatment. There was a significant correlation of urinary activin A level with urinary protein, L-FABP, and NAG. Histologic evaluation revealed that urinary activin A levels were significantly higher in patients with cellular crescentic glomeruli than in those lacking this damage. In situ hybridization demonstrated that the mRNA encoding the activin A βA subunit was undetectable in normal kidneys but accumulated in the proximal tubules and crescentic glomeruli of the kidneys of patients with renal AAV. Immunostaining showed that activin A protein also was present in the proximal tubules, crescentic glomeruli, and macrophages infiltrating into the interstitium in the kidneys of patients with renal AAV. These data suggested that urinary activin A concentration reflects renal inflammation and tubular damage in AAV and may be a useful biomarker for monitoring renal AAV.
Acute kidney injury (AKI) is a common but complex condition that is associated with increased morbidity and mortality. In the present study, we examined whether urinary activin A, a member of the ...TGF-beta superfamily, is present in mice with ischemia-reperfusion injury and in humans with AKI, as well as its potential as a biomarker for AKI. Expression of activin A was markedly increased in ischemic mouse kidneys. In situ hybridization demonstrated that activin mRNA was expressed in tubular cells of ischemic kidneys but not of normal kidneys. Immunoreactive activin A, which was absent in normal kidneys, was detected in the cytoplasm of proximal tubular cells in ischemic kidneys. Activin A was undetectable in the urine of normal mice. In contrast, activin A was significantly increased in the urine of ischemic mice at 3 h after reperfusion. Urinary activin A levels increased according to the period of ischemia. In humans, urinary activin A was almost undetectable in healthy volunteers and in patients with pre-renal AKI, but was significantly increased in patients with renal AKI. There was no significant correlation between urinary activin A and serum activin A. Collectively, urinary activin A might be a useful biomarker reflecting the severity of AKI.
Summary To further clarify the molecular features of colorectal neuroendocrine carcinomas (NECs), we immunohistochemically examined tumor samples from 25 NECs, including 9 small cell NECs (SCNECs) ...and 16 large cell NECs (LCNECs), 20 neuroendocrine tumors (NETs), and 21 poorly differentiated adenocarcinomas (PDCs) for the expression of several biomarkers (p53, β -catenin, Bcl-2, Rb, p16, p21, cyclin D1, and cyclin E) and used sequencing analysis to identify gene alterations of TP53 , APC , CTNNB1 , KRAS , and BRAF . The frequencies of aberrant p53 expression (88%), β -catenin nuclear expression (48%), and high expression of cyclin E (84%) were significantly higher in NECs than in NETs (0%, 5%, and 5%, P < .01, respectively). The immunohistochemical results of NECs and PDCs were similar. TP53 , APC , KRAS , and BRAF gene mutations were variously detected in NECs and PDCs but not in any NETs. The frequencies of decreased expression of Rb (56%) and high expression of p16 (56%) and Bcl-2 (64%) were significantly higher in NECs than in PDCs (5%, 19%, and 5%, P < .05, respectively) or NETs (10%, 5%, and 5%, P < .01, respectively). Such immunohistochemical characteristics of NECs were more evident in SCNECs than in large cell NECs ( P < .01). In conclusion, the molecular features of colorectal NECs are similar to those of adenocarcinomas and not to those of NETs. Decreased expression of Rb and high expression of p16 and Bcl-2 are characteristics of NECs, suggesting that Rb-p16 pathway disruption may contribute to the promotion of proliferative activity in colorectal NECs. SCNECs may be a prototype of NECs.
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