Knocking out a specific tRNA species within unfractionated Escherichia coli tRNA by using antisense (complementary) oligodeoxyribonucleotides

Methods for the preparation of an Escherichia coli tRNA mixture lacking one or a few specific tRNA species can be the basis for future applications of cell-free protein synthesis. We demonstrate here that virtually a single tRNA species in a crude E. coli tRNA mixture can be knocked out by an antisense (complementary) oligodeoxyribonucleotide. One out of five oligomers complementary to tRNA^Asp blocked the aspartylation almost completely, while minimally affecting the aminoacylation with other 13 amino acids tested. This `knockout' tRNA behaved similarly to the untreated tRNA in a cell-free translation of an mRNA lacking Asp codons.     

The characteristics of encapsulated whole cell β-galactosidase

We prepared encapsulated whole cell β-galactosidase using E. coli. The cell culture was divided into two steps for the cell accumulation inside the capsule and enzyme production in the cell. Growth and production media were used individually for this purpose. The dry cell weight of the free cell culture was increased 2.8 times by controlling the pH of the growth medium during cultivation. However, the weight of cells accumulated in the capsule reduced 40% with pH control. The dry cell weight increased with lactose concentration of the production medium for both cases of free and capsule cultures. The dry cell weights were 1.5?g/l for free culture and 100?g/l in the capsule when the lactose concentration of the production medium was 10?g/l. The dry cell weight increased about 60% for both cases as the lactose concentration increased from 10 to 50?g/l. The specific activity of whole cell enzyme decreased with lactose concentration from 5 to 1.4?unit/g dry cell for free culture and from 1.1 to 0.65?unit/g dry cell in the capsule. The value of Michaelis constant, K_m, of whole cell enzyme increased 3 times because of the resistance of mass transfer through the capsule membrane. The constants of Michaelis-Menten equation for the whole cell enzyme in the capsule were V_m: 0.0479?mM/min and K_m: 44.86?mM. These constants of the membrane-free cells were V_m: 0.0464?mM/min and K_m: 15.64?mM. To increase the whole cell enzyme activity, we treated encapsulated cells with organic solvents. The activity of encapsulated whole cell enzyme was increased 3.5 times with the treatment of chloroform and ethanol. The activity of the encapsulated whole cell enzymes was reserved after repeating the process 30 times.     

Target proteins of the cytosolic thioredoxin in Plasmodium falciparum

The target proteins of a cytosolic Trx (PfTrx-1) in Plasmodium falciparum with Trx-affinity chromatography were examined. Based on the Trx protein reduction pathway, we generated a cysteine mutant of PfTrx-1, which captures the target protein as a mixed disulfide intermediate. A number of proteins were captured with PfTrx-1(C33S) immobilized on resin and were eluted by DTT treatment. The PfTrx-1(C33S) immobilized resin-captured proteins were trypsin-digested and analyzed on a liquid chromatography-mass spectrometry system. Analysis of the sequence data against databases assigned 20 proteins, four of which had been found previously in P. falciparum, with the remaining 16 being new targets. The potential Trx-target proteins included those in pathways such as the redox cycle, protein biosynthesis, energy metabolism and signal transduction. We captured 4 enzymes in the glycolysis pathway (hexokinase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate mutase and l-lactate dehydrogenase (LDH)) as Trx-targets, and we found that PfTrx-1 enhanced the activity of PfGAPDH and PfLDH.     

Investigation of Susceptibility Genes Triggering Lachrymal/Salivary Gland Lesion Complications in Japanese Patients with Type 1 Autoimmune Pancreatitis

Autoimmune pancreatitis (AIP) is a unique form of chronic pancreatitis characterized by high serum IgG4 concentration and a variety of complicating extra-pancreatic lesions. In particular, lachrymal/salivary gland lesions tend to manifest in a highly active AIP disease state, and several genes are speculated to be associated with the onset of this complication. We therefore searched for candidate susceptibility genes related to lachrymal/salivary gland lesions in a genome-wide association study (GWAS) with the GeneChip Human Mapping 500k Array Set (Affymetrix, CA) that was followed by fine mapping of additional single nucleotide polymorphisms (SNPs) in strongly significant genes with TaqMan assays. Venous blood samples were obtained from 50 type 1 AIP patients with lachrymal/salivary gland lesions (A group) and 53 type 1 AIP patients without (B group). The mean values of IgG and IG4 were both significantly different (P<0.05) between the groups. SNPs that showed a significant association with the A group at the genome-wide level (P<0.0001) were identified and subsequently used in fine SNP mapping of candidate genes. In total, five SNPs had a positive association with complicated AIP (most notably rs2284932 [P=0.0000021]) and five SNPs possessed a negative association (particularly rs9371942 [P=0.00000039]). Among them, KLF7, FRMD4B, LOC101928923, and MPPED2 were further examined for complication susceptibility using additional SNPs that were not included in the GWAS. Individual genotyping of KLF7 rs2284932 revealed that the frequency of the minor C allele was significantly increased (P=0.00062, Pc=0.0018, OR=2.98, 95%CI=1.58-5.65) in group A. The minor T allele of rs4473559 in FRMD4 demonstrated a significant association in the A group (P=0.00015, OR=3.38, 95%CI=1.77-7.65). In the LOC101928923 gene, the frequency of the minor C allele of rs4379306 was significantly decreased in group A in both TaqMan and GWAS analyses. Lastly, the minor C allele of MPPED2 rs514644 carried a significantly increased risk of complications. These four genes may be linked with the onset of lachrymal/salivary gland lesions in type 1 AIP patients and require further study.     

Nasal Lipopolysaccharide Challenge and Cytokine Measurement Reflects Innate Mucosal Immune Responsiveness

Background

Practical methods of monitoring innate immune mucosal responsiveness are lacking. Lipopolysaccharide (LPS) is a component of the cell wall of Gram negative bacteria and a potent activator of Toll-like receptor (TLR)-4. To measure LPS responsiveness of the nasal mucosa, we administered LPS as a nasal spray and quantified chemokine and cytokine levels in mucosal lining fluid (MLF).

Methods

We performed a 5-way cross-over, single blind, placebo-controlled study in 15 healthy non-atopic subjects (n = 14 per protocol). Doses of ultrapure LPS (1, 10, 30 or 100μg/100μl) or placebo were administered by a single nasal spray to each nostril. Using the recently developed method of nasosorption with synthetic adsorptive matrices (SAM), a series of samples were taken. A panel of seven cytokines/chemokines were measured by multiplex immunoassay in MLF. mRNA for intercellular cell adhesion molecule-1 (ICAM-1) was quantified from nasal epithelial curettage samples taken before and after challenge.

Results

Topical nasal LPS was well tolerated, causing no symptoms and no visible changes to the nasal mucosa. LPS induced dose-related increases in MLF levels of IL-1β, IL-6, CXCL8 (IL-8) and CCL3 (MIP-1α) (AUC at 0.5 to 10h, compared to placebo, p<0.05 at 30 and 100μg LPS). At 100μg LPS, IL-10, IFN-α and TNF-α were also increased (p<0.05). Dose-related changes in mucosal ICAM-1 mRNA were also seen after challenge, and neutrophils appeared to peak in MLF at 8h. However, 2 subjects with high baseline cytokine levels showed prominent cytokine and chemokine responses to relatively low LPS doses (10μg and 30μg LPS).

Conclusions

Topical nasal LPS causes dose-dependent increases in cytokines, chemokines, mRNA and cells. However, responsiveness can show unpredictable variations, possibly because baseline innate tone is affected by environmental factors. We believe that this new technique will have wide application in the study of the innate immune responses of the respiratory mucosa.

Key Messages

Ultrapure LPS was used as innate immune stimulus in a human nasal challenge model, with serial sampling of nasal mucosal lining fluid (MLF) by nasosorption using a synthetic absorptive matrix (SAM), and nasal curettage of mucosal cells. A dose response could be demonstrated in terms of levels of IL-1β, IL-6, CXCL8 and CCL3 in MLF, as well as ICAM-1 mRNA in nasal curettage specimens, and levels of neutrophils in nasal lavage. Depending on higher baseline levels of inflammation, there were occasional magnified innate inflammatory responses to LPS.

Trial Registration

Clinical Trials.gov NCT02284074     

Increase in Ultrasonic Intensity of Blood Speckle across Moderate Coronary Artery Stenosis Is an Independent Predictor of Functional Coronary Artery Stenosis Measured by Fractional Flow Reserve: Pilot Study

Background and Aims

The degree of coronary artery stenosis should be assessed both anatomically and functionally. We observed that the intensity of blood speckle (IBS) on intravascular ultrasound (IVUS) is low proximal to a coronary artery stenosis, and high distal to the stenosis. We defined step-up IBS as the distal minus the proximal IBS, and speculated that this new parameter could be used for the functional evaluation of stenosis on IVUS. The aims of this study were to assess the relationships between step-up IBS and factors that affect coronary blood flow, and between step-up IBS and fractional flow reserve (FFR).

Methods and Results

This study enrolled 36 consecutive patients with angina who had a single moderate stenosis in the left anterior descending artery. All patients were evaluated by integrated backscatter IVUS and intracoronary pressure measurements. FFR was calculated from measurements using a coronary pressure wire during hyperemia. Conventional gray-scale IVUS images were recorded, and integrated backscatter was measured in three cross-sectional slices proximal and distal to the stenosis. Step-up IBS was calculated as (mean distal integrated backscatter value) − (mean proximal integrated backscatter value). Stepwise multiple linear regression analysis showed that the heart rate (r = 0.45, P = 0.005), ejection fraction (r = −0.39, P = 0.01), and hemoglobin level (r = −0.32, P = 0.04) were independently correlated with step-up IBS, whereas proximal and distal IBS were not associated with these factors. There was a strong inverse correlation between step-up IBS and FFR (r = −0.84, P < 0.001), which remained significant on stepwise multiple linear regression analysis.

Conclusions

The newly defined parameter of step-up IBS is potentially useful for the functional assessment of coronary artery stenosis.     

Effect of reactor surface on production of bacterial cellulose and water soluble oligosaccharides by <Emphasis Type="Italic">Gluconacetobacter hansenii</Emphasis> PJK

The effect of agar plates on the bacterial cellulose (BC) production in a static culture was investigated in order to find the role of agar component as a surface modifying agent. Two types of surface modified reactors (SMRs: SMRD and SMRB) were prepared by coating the bottom of the reactors with agar dissolved in distilled water and basal medium, respectively. The SMRs were used for BC and water soluble oligosaccharides (WSOS) production. Control was done by the same procedure using reactors without agar plate. In both types of SMRs, the maximum production rate was observed after the second day of cultivation compared to third day of cultivation in the case of the control. The maximum productions of BC 5.308 and 5.472 g/L were observed at the first batch using SMRs prepared with agar dissolved in distilled water (SMRDs) and SMRs prepared with agar dissolved in a basal medium (SMRBs), respectively. Similarly, in the daily-culture and successive batch strategy experiments the maximum amount of WSOS produced in the SMRs was almost double that of the control. The highest water holding capacity value 92.21 g/g was observed for BC formed in the SMRs prepared with 3.0% of agar. FTIR and XRD analyses were carried out to study the structural features of the prepared BC.