Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli.

The Escherichia coli ygjD gene is critical for the universal tRNA modification N(6)-threonylcarbamoyladenosine, together with two other essential genes, yeaZ and yjeE. This study showed that the transcription of the thr and ilv operons in ygjD mutants was increased through the inhibition of transcription attenuation and that dnaG transcription was reduced.

Knowledge Learning of Replacement Judgment Using Word-of-mouth Data.

The pandemic caused by COVID-19 has also affected the camera industry, and various events have been cancelled. In addition, the recent improvement in the performance of cameras installed in smartphones has reduced the demand for replacement cameras, as it is easy to take pictures without carrying a camera. For customers, online word-of-mouth is what they refer to when purchasing a product. This data is important not only for customers, but also for companies. In this research, we will use online word-of-mouth data and focus not only on numerical data but also on textual data and use text mining to learn knowledge about the decision to replace a camera.

Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites.

Plant-biosynthesised secondary metabolites are unique sources of pharmaceuticals, food additives, and flavourings, among other industrial uses. However, industrial production of these metabolites is difficult because of their structural complexity, dangerousness and unfriendliness to natural environment, so the development of new methods to synthesise them is required. In this study, we developed a novel approach to identifying alternative bacterial enzyme to produce plant-biosynthesised secondary metabolites. Based on the similarity of enzymatic reactions, we searched for candidate bacterial genes encoding enzymes that could potentially replace the enzymes in plant-specific secondary metabolism reactions that are contained in the KEGG database (enzyme re-positioning). As a result, we discovered candidate bacterial alternative enzyme genes for 447 plant-specific secondary metabolic reaction. To validate our approach, we focused on the ability of an enzyme from Streptomyces coelicolor strain A3(2) strain to convert valencene to the grapefruit metabolite nootkatone, and confirmed its enzymatic activity by gas chromatography-mass spectrometry. This enzyme re-positioning approach may offer an entirely new way of screening enzymes that cannot be achieved by most of other conventional methods, and it is applicable to various other metabolites and may enable microbial production of compounds that are currently difficult to produce industrially.

Analysis of Dietary Factors Affecting Body Mass Index in Elderly Patients With Type 2 Diabetes Mellitus.

BACKGROUND: Body mass index (BMI) is correlated with the outcomes of various metabolic and pathological conditions. To elucidate the factors affecting BMI in elderly persons, we studied elderly persons with and without diabetes mellitus for BMI management target values using receiver operating characteristic (ROC) analysis. METHODS: We conducted a dietary survey targeting 60 elderly outpatients with type 2 diabetes mellitus (diabetes group, 70.1 ± 7.8 years) and 66 elderly persons who participated in a health class offered by the municipality (health class group, 72.5 ± 5.7 years). RESULTS: In the diabetes group, positive correlations were observed between BMI and several variables including blood glucose levels (all P < 0.05), whereas BMI had negative correlations with the third principal component (positive weight for oils and fats). In addition, BMI was negatively correlated with the intake of oils and fats. In the health class group, BMI was positively correlated (all P < 0.05) with grip strength/sixth principal component (positive weight for sweets)/condiments. An analysis of dietary patterns revealed that dietary factors correlated with BMI in each group. The cutoff value of BMI was suggested to be near the normal upper limit or slightly higher in the subject group. CONCLUSION: We considered that BMI management was useful as an indicator for maintaining grip and muscle strength in elderly persons and as an indicator for diabetes care management. From the present study, we may propose the utility of a careful dietary survey as one of the approaches for these aims.

The utility of nutritional supportive care with an eicosapentaenoic acid (EPA)-enriched nutrition agent during pre-operative chemoradiotherapy for pancreatic cancer: Prospective randomized control study.

BACKGROUND & AIMS: Neoadjuvant chemoradiotherapy (NACRT) for pancreatic cancer (PC) is potentially associated with various toxicities, which can lead to impaired nutritional status. Eicosapentaenoic acid (EPA) can reduce proinflammatory cytokines and positively influence cancer cachexia syndrome. The aim of this study is to clarify the utility of EPA enriched nutrition support during NACRT for PC. METHODS: We randomly assigned 62 patients with PC that received NACRT to either a nutrition intervention (NI) or a normal diet (ND). Patients in the NI group received 2 bottles/day (550 kcal/day) of an EPA-enriched nutrition supplement during NACRT. The primary endpoints were the before-to-after NACRT ratios (post/pre ratios) of skeletal muscle mass and psoas major muscle area (PMA). The secondary endpoints were the post/pre ratios of other nutritional parameters and treatment-related toxicities. RESULTS: Only 14 patients (45.2%) in the NI group consumed more than 50% of the EPA-enriched supplement provided. The post/pre ratio of skeletal muscle mass in the NI group (0.99 ± 0.060) was not significantly different from that of the ND group (0.96 ± 0.079, p = 0.102). However, patients that consumed ≥50% of the EPA-enriched supplement (the good intake group) had significantly higher skeletal muscle mass ratios than patients in the ND group (p = 0.042). The PMA ratio was significantly higher in the NI group (0.96 ± 0.081) than in the ND group (0.89 ± 0.072, p = 0.001). The NI and ND groups were not significantly different in other nutritional parameters or in NACRT-related toxicity. CONCLUSIONS: We found that EPA-enriched intake could potentially improve the nutritional status of patients with PC that received NACRT, but it was difficult for many patients to drink, due to its disagreeable taste. University Hospital Medical Information Network (http://www.umin.ac.jp), registration number UMIN000033589, https://upload.umin.ac.jp/cgi-bin/ctr_e/ctr_view.cgi?recptno=R000038300.

Relationship between Food-Intake Trends and Estimated Glomerular Filtration Rate in Elderly Patients with Type 2 Diabetes Mellitus.

The aim of this study is to investigate how vegetable and fruit intake trends affect the estimated glomerular filtration rate (eGFR) by analyzing therapeutic diet status in elderly type 2 diabetes mellitus patients. The study included 59 elderly patients with type 2 diabetes mellitus (mean age: 70.1±7.8 y) who had previously received therapeutic education for type 2 diabetes mellitus from a clinical team and were subsequently receiving outpatient treatment. Blood examination data were retrospectively collected from medical records and diet status was investigated using a simplified self-administered diet history questionnaire. Dietary patterns were extracted using principal component analysis, and the relationships with each blood examination data were investigated. Linear regression analysis was then used to examine the intake food groups related to eGFR. Energy intake was 27±9 kcal/kg. Overall, these results were in line with the Guidelines for the Treatment of Diabetes in Japan 2016. As a result of principal component analysis, seven dietary patterns were extracted, and the cumulative contribution ratio of the seven components was 74.0%. Among the dietary patterns, the 6th factor (positive weighting with fruit) for eGFR was a negative prognostic factor (p=0.010). Analysis of food group intake and eGFR indicated that green and yellow vegetables were positive prognostic factors, whereas fruits were negative prognostic factors (both p<0.05). The dietary patterns dependent on green and yellow vegetables and fruit intake appeared to influence eGFR positively and negatively, respectively.

Identification of NAP1, a regulatory subunit of IkappaB kinase-related kinases that potentiates NF-kappaB signaling.

The IkappaB kinase (IKK)-related kinase NAK (also known as TBK or T2K) contributes to the activation of NF-kappaB-dependent gene expression. Here we identify NAP1 (for NAK-associated protein 1), a protein that interacts with NAK and its relative IKK epsilon (also known as IKKi). NAP1 activates NAK and facilitates its oligomerization. Interestingly, the NAK-NAP1 complex itself effectively phosphorylated serine 536 of the p65/RelA subunit of NF-kappaB, and this activity was stimulated by tumor necrosis factor alpha (TNF-alpha). Overexpression of NAP1 specifically enhanced cytokine induction of an NF-kappaB-dependent, but not an AP-1-dependent, reporter. Depletion of NAP1 reduced NF-kappaB-dependent reporter gene expression and sensitized cells to TNF-alpha-induced apoptosis. These results define NAP1 as an activator of IKK-related kinases and suggest that the NAK-NAP1 complex may protect cells from TNF-alpha-induced apoptosis by promoting NF-kappaB activation.

[A Japanese case of melioidosis presenting as multiple organ lesions accompanied by sepsis and disseminated intravascular coagulation, after a visit to Thailand].

A 65-year-old man with diabetes mellitus reporting fever and urination disturbance on a flight from Bangkok back to Japan in July 2003 was admitted elsewhere for acute prostatitis. Despite intravenous antibiotics, his condition deteriorated. On admission to our hospital, he suffered from respiratory failure, with laboratory data showing disseminated intravascular coagulation (DIC). Computed tomography (CT) shows infiltrative and nodular shadows in both lung fields and low-density areas in the left kidney and prostate gland, consistent with pneumonia and abscesses in these organs. He also developed broad osteomyelitis in the right lower extremity with cellulitis and arthritis in the right hand, knee, and foot. Blood, urine, and joint fluid culture all yielded Burkholderia pseudomallei, so he was diagnosed with melioidosis. Treatment was started with meropenem and minocycline, then meropenem was changed to imipenem. His symptoms gradually improved after ciprofloxacin was added, so all intravenous antibiotics were discontinued and he underwent oral treatment with chloramphenicol, minocycline, and sulfamethoxazole/trimethoprim in September 2003. He developed fever again, however, and oral therapy was discontinued and intravenous antibiotics restarted. After resolution of fever, oral maintenance therapy was initiated again with levofloxacin and minocycline in October, and his condition remained stable. After discharge in April 2004, he has been followed up with no evidence of relapse. This is considered to be the seventh case of melioidosis reported in Japan. Our patient manifested multiple organ lesions with sepsis and DIC, and was difficult to treat, but clinical symptoms improved in long-term antibiotic administration. With travelers to Southeast Asia increasing, greater attention must be paid to imported infectious diseases, such as melioidosis.

The Effectiveness of a Liver Disease Education Class for Providing Information to Patients and Their Families.

BACKGROUND: We have been conducting liver disease education classes regularly in our hospital for the purpose of providing health information to patients and their families. METHODS: In order to evaluate the effectiveness of these classes, we conducted a questionnaire survey of patients and family members who attended the classes held three times in 2012. The cumulative total number of participants was 80 (49 patients, 26 family members, and five others). The classes focused on the following areas: 1) prevention of hepatic cancer; 2) treatment of hepatic cancer; 3) iron restriction diet for hepatitis C patients; and 4) importance of branched-chain amino acid preparations. Self-evaluation of knowledge in these areas was based on a four-point scale. RESULTS: A comparison of knowledge levels between the patients and their family members revealed no statistically significant differences. Therefore, subsequent analyses were performed by combining the patients and their families into one group. The knowledge level of the participants increased with the number of class attendances; that is, the more often they attended, the more they accumulated knowledge (Kruskal-Wallis test: P < 0.0001; P = 0.0368; P = 0.0021; and P < 0.0001). In addition, the results of the questionnaire administered immediately before and after the education class showed significant improvement in the knowledge level for each area. CONCLUSION: The results of this study indicate the liver disease education class to be effective for improving the knowledge of patients and their families. The importance of repeated information provision was also demonstrated.

Identification of aberrantly methylated genes in association with adult T-cell leukemia.

In this study, we identified 53 aberrantly hypermethylated DNA sequences in adult T-cell leukemia (ATL) cells using methylated CpG island amplification/representational difference analysis method. We also observed a proportionate increase in the methylation density of these regions with disease progression. Seven genes, which were expressed in normal T cells, but suppressed in ATL cells, were identified near the hypermethylated regions. Among these silenced genes, Kruppel-like factor 4 (KLF4) gene is a cell cycle regulator and early growth response 3 (EGR3) gene is a critical transcriptional factor for induction of Fas ligand (FasL) expression. Treatment with 5-aza-2'-deoxycytidine resulted in the recovery of their transcription, indicating that their silencing might be associated with DNA hypermethylation. To study their functions in ATL cells, we transfected recombinant adenovirus vectors expressing KLF4 and EGR3 genes. Expression of KLF4 induced apoptosis of ATL cells whereas enforced expression of EGR3 induced the expression of FasL gene, resulting in apoptosis. Thus, suppressed expression of EGR3 enabled ATL cells to escape from activation-induced cell death mediated by FasL. Our results showed that the methylated CpG island amplification/representational difference analysis method allowed the isolation of hypermethylated DNA regions specific to leukemic cells and thus shed light on the roles of DNA methylation in leukemogenesis.

Silencing of human T-cell leukemia virus type I gene transcription by epigenetic mechanisms.

BACKGROUND: Human T-cell leukemia virus type I (HTLV-I) causes adult T-cell leukemia (ATL) after a long latent period. Among accessory genes encoded by HTLV-I, the tax gene is thought to play a central role in oncogenesis. However, Tax expression is disrupted by several mechanims including genetic changes of the tax gene, deletion/hypermethylation of 5'-LTR. To clarify the role of epigenetic changes, we analyzed DNA methylation and histone modification in the whole HTLV-I provirus genome. RESULTS: The gag, pol and env genes of HTLV-I provirus were more methylated than pX region, whereas methylation of 5'-LTR was variable and 3'-LTR was not methylated at all. In ATL cell lines, complete DNA methylation of 5'-LTR was associated with transcriptional silencing of viral genes. HTLV-I provirus was more methylated in primary ATL cells than in carrier state, indicating the association with disease progression. In seroconvertors, DNA methylation was already observed in internal sequences of provirus just after seroconversion. Taken together, it is speculated that DNA methylation first occurs in the gag, pol and env regions and then extends in the 5' and 3' directions in vivo, and when 5'-LTR becomes methylated, viral transcription is silenced. Analysis of histone modification in the HTLV-I provirus showed that the methylated provirus was associated with hypoacetylation. However, the tax gene transcript could not be detected in fresh ATL cells regardless of hyperacetylated histone H3 in 5'-LTR. The transcription rapidly recovered after in vitro culture in such ATL cells. CONCLUSION: These results showed that epigenetic changes of provirus facilitated ATL cells to evade host immune system by suppressing viral gene transcription. In addition, this study shows the presence of another reversible mechanism that suppresses the tax gene transcription without DNA methylation and hypoacetylated histone.

Genetic subtypes of HIV type 1 based on the vpu/env sequences in the Republic of Congo.

To investigate the HIV-1 subtypes prevalent in the Republic of Congo, we isolated 28 HIV-1 strains from Congolese AIDS patients in 1996 and 1997, and analyzed them phylogenetically. Phylogenetic analysis based on part of the 5' tat-env (vpu) and env sequences revealed that only 13 (46.4%) of the 28 isolates belonged to the same subtype in the vpu tree as in the env tree; the remaining 15 (53.6%) strains showed discordant subtypes between vpu and env with 6 different profiles; that is, 1 A/A (vpu/env), 1 D/D, 5 G/G, 4 H/H, 2 unclassified (U)/U, 9 G/A, 2 G/H, 1 G/J, 1 H/G, 1 U/A, and 1 U/J. Thus, 9 of the 15 discordant HIV-1s were of the G/A (vpu/env) type, and did not form any subcluster within the subtype G lineage in the vpu-based phylogenetic tree. In addition, CRF02_AG (IbNG), which is a G/A (vpu/env) type, was not found in the Republic of Congo. These data suggest that the majority of HIV-1 subtypes circulating in the Republic of Congo have mosaic structures and may have been derived from independent recombinational events.

Preferential selection of human T-cell leukemia virus type 1 provirus lacking the 5' long terminal repeat during oncogenesis.

In adult T-cell leukemia (ATL) cells, a defective human T-cell leukemia virus type 1 (HTLV-1) provirus lacking the 5' long terminal repeat (LTR), designated type 2 defective provirus, is frequently observed. To investigate the mechanism underlying the generation of the defective provirus, we sequenced HTLV-1 provirus integration sites from cases of ATL. In HTLV-1 proviruses retaining both LTRs, 6-bp repeat sequences were adjacent to the 5' and 3' LTRs. In 8 of 12 cases with type 2 defective provirus, 6-bp repeats were identified at both ends. In five of these cases, a short repeat was bound to CA dinucleotides of the pol and env genes at the 5' end, suggesting that these type 2 defective proviruses were formed before integration. In four cases lacking the 6-bp repeat, short (6- to 26-bp) deletions in the host genome were identified, indicating that these defective proviruses were generated after integration. Quantification indicated frequencies of type 2 defective provirus of less than 3.9% for two carriers, which are much lower than those seen for ATL cases (27.8%). In type 2 defective proviruses, the second exons of the tax, rex, and p30 genes were frequently deleted, leaving Tax unable to activate NF-kappaB and CREB pathways. The HTLV-1 bZIP factor gene, located on the minus strand, is expressed in ATL cells with this defective provirus, and its coding sequences are intact, suggesting its significance in oncogenesis.

De novo human T-cell leukemia virus type 1 infection of human lymphocytes in NOD-SCID, common gamma-chain knockout mice.

Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia, a disease that is triggered after a long latency period. HTLV-1 is known to spread through cell-to-cell contact. In an attempt to study the events in early stages of HTLV-1 infection, we inoculated uninfected human peripheral blood mononuclear cells and the HTLV-1-producing cell line MT-2 into NOD-SCID, common gamma-chain knockout mice (human PBMC-NOG mice). HTLV-1 infection was confirmed with the detection of proviral DNA in recovered samples. Both CD4+ and CD8+ T cells were found to harbor the provirus, although the latter population harbored provirus to a lesser extent. Proviral loads increased with time, and inverse PCR analysis revealed the oligoclonal proliferation of infected cells. Although tax gene transcription was suppressed in human PBMC-NOG mice, it increased after in vitro culture. This is similar to the phenotype of HTLV-1-infected cells isolated from HTLV-1 carriers. Furthermore, the reverse transcriptase inhibitors azidothymidine and tenofovir blocked primary infection in human PBMC-NOG mice. However, when tenofovir was administered 1 week after infection, the proviral loads did not differ from those of untreated mice, indicating that after initial infection, clonal proliferation of infected cells was predominant over de novo infection of previously uninfected cells. In this study, we demonstrated that the human PBMC-NOG mouse model should be a useful tool in studying the early stages of primary HTLV-1 infection.

Preferential selection of human T-cell leukemia virus type I provirus integration sites in leukemic versus carrier states.

Human T-cell leukemia virus type I (HTLV-I) is a causative agent of neoplastic disease, adult T-cell leukemia (ATL). Although the encoding viral proteins play an important role in oncogenesis, the role of the HTLV-I proviral integration site remains unsolved. We determined the integration sites of HTLV-I proviruses in ATL cells and HTLV-I-infected cells in asymptomatic carriers. In carrier and ATL cells, HTLV-I provirus was integrated into the transcriptional unit at frequencies of 26.8% (15/56) and 33.9% (20/59), respectively, which were equivalent to the frequency calculated based on random integration (33.2%). In addition, HTLV-I provirus was prone to integration near the transcriptional start sites in leukemic cells (P = .006), and the transcriptional direction of the provirus was in accordance with that of integrated cellular genes in 70% of cases. More importantly, the integration sites in the carrier cells favored the alphoid repetitive sequences (11/56; 20%) whereas in leukemic cells they disfavored these sequences (2/59; 3.4%). Taken together, during natural course from carrier to onset of ATL, HTLV-I-infected cells with integration sites favorable for viral gene transcription are susceptible to malignant transformation due to increased viral gene expression.

Genetic and epigenetic inactivation of tax gene in adult T-cell leukemia cells.

To clarify the status of tax gene, we analyzed human T-cell leukemia virus type-I (HTLV-I) associated cell lines and fresh adult T-cell leukemia (ATL) cells. We compared 2 types of HTLV-I associated cell lines: one was derived from leukemic cells (leukemic cell line) and the other from nonleukemic cells (nonleukemic cell line). Although all nonleukemic cell lines expressed Tax, it could not be detected in 3 of 5 leukemic cell lines, in which nonsense mutation or deletion (60 bp) of tax genes, and DNA methylation in 5'-LTR were identified as the responsible changes. We found such genetic changes of the tax gene in 5 of 47 fresh ATL cases (11%). The tax gene transcripts could be detected in 14 of 41 fresh ATL cases (34%) by RT-PCR. In ATL cases with genetic changes that could not produce Tax protein, the tax gene was frequently transcribed, suggesting that such cells do not need the transcriptional silencing. Although DNA methylation of 5'-LTR was detected in the fresh ATL cases (19 of 28 cases; 68%), the complete methylation associated with transcriptional silencing was observed only in 4 cases. Since partial methylation could not silence the transcription, and the tax gene transcription was not detected in 27 of 41 cases (66%), the epigenetic change(s) other than DNA methylation is considered to play an important role in the silencing.