High-resolution mapping of plasmid transcriptomes in different host bacteria

<p>Abstract</p> <p>Background</p> <p>Plasmids are extrachromosomal elements that replicate autonomously, and many can be transmitted between bacterial cells through conjugation. Although the transcription pattern of genes on a plasmid can be altered by a change in host background, the expression range of plasmid genes that will result in phenotypic variation has not been quantitatively investigated.</p> <p>Results</p> <p>Using a microarray with evenly tiled probes at a density of 9 bp, we mapped and quantified the transcripts of the carbazole catabolic plasmid pCAR1 in its original host <it>Pseudomonas resinovorans </it>CA10 and the transconjugant <it>P</it>. <it>putida </it>KT2440(pCAR1) during growth on either carbazole or succinate as the sole carbon source. We identified the operons in pCAR1, which consisted of nearly identical transcription units despite the difference in host background during growth on the same carbon source. In accordance with previous studies, the catabolic operons for carbazole degradation were upregulated during growth on carbazole in both hosts. However, our tiling array results also showed that several operons flanking the transfer gene cluster were transcribed at significantly higher levels in the transconjugant than in the original host. The number of transcripts and the positions of the transcription start sites agreed with our quantitative RT-PCR and primer extension results.</p> <p>Conclusion</p> <p>Our tiling array results indicate that the levels of transcription for the operons on a plasmid can vary by host background. High-resolution mapping using an unbiased tiling array is a valuable tool for the simultaneous identification and quantification of prokaryotic transcriptomes including polycistronic operons and non-coding RNAs.</p

Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids

Bacterial nucleoid-associated proteins (NAPs) form nucleoprotein complexes and influence the expression of genes. Recent studies have shown that some plasmids carry genes encoding NAP homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. In this study, we determined the distributions of the well-known NAPs Fis, H-NS, HU, IHF, and Lrp and the newly found NAPs MvaT and NdpA among the whole-sequenced 1382 plasmids found in Gram-negative bacteria. Comparisons between NAP distributions and plasmid features (size, G+C content, and putative transferability) were also performed. We found that larger plasmids frequently have NAP gene homologs. Plasmids with H-NS gene homologs had less G+C content. It should be noted that plasmids with the NAP gene homolog also carried the relaxase gene involved in the conjugative transfer of plasmids more frequently than did those without the NAP gene homolog, implying that plasmid-encoded NAP homologs positively contribute to transmissible plasmids

Independent calculation-based verification of volumetric-modulated arc therapy–stereotactic body radiotherapy plans for lung cancer

This study aimed to investigate the feasibility of independent calculation‐based verification of volumetric‐modulated arc therapy (VMAT)–stereotactic body radiotherapy (SBRT) for patients with lung cancer using a secondary treatment planning system (sTPS). In all, 50 patients with lung cancer who underwent VMAT‐SBRT between April 2018 and May 2019 were included in this study. VMAT‐SBRT plans were devised using the Collapsed‐Cone Convolution in RayStation (primary TPS: pTPS). DICOM files were transferred to Eclipse software (sTPS), which utilized the Eclipse software, and the dose distribution was then recalculated using Acuros XB. For the verification of dose distribution in homogeneous phantoms, the differences among pTPS, sTPS, and measurements were evaluated using passing rates of a dose difference of 5% (DD5%) and gamma index of 3%/2 mm (γ3%/2 mm). The ArcCHECK cylindrical diode array was used for measurements. For independent verification of dose‐volume parameters per the patient’s geometry, dose‐volume indices for the planning target volume (PTV) including D95% and the isocenter dose were evaluated. The mean differences (± standard deviations) between the pTPS and sTPS were then calculated. The gamma passing rates of DD5% and γ3%/2 mm criteria were 99.2 ± 2.4% and 98.6 ± 3.2% for pTPS vs. sTPS, 92.9 ± 4.0% and 94.1 ± 3.3% for pTPS vs. measurement, and 93.0 ± 4.4% and 94.3 ± 4.1% for sTPS vs. measurement, respectively. The differences between pTPS and sTPS for the PTVs of D95% and the isocenter dose were −3.1 ± 2.0% and −2.3 ± 1.8%, respectively. Our investigation of VMAT‐SBRT plans for lung cancer revealed that independent calculation‐based verification is a time‐efficient method for patient‐specific quality assurance

Desempeños del alumnado de Educación Secundaria en la evaluación de una investigación científica en el contexto de la industria láctea

En este estudio se analizan los desempeños de estudiantes de 2.º, 3.º y 4.º de ESO (14, 15 y 16 años) que cursan la asignatura de Física y química, cuando evalúan el diseño de una investigación sobre un problema de precipitación identificado en la industria láctea. Los desempeños se examinan por separado para cada dimensión del diseño: identificación de la cuestión objeto de investigación, formulación de hipótesis, planificación de la investigación y selección del criterio de finalización. Para el análisis de resultados, se recogen sus propuestas, en las que han de estar desarrolladas las siguientes tareas: seleccionar la mejor opción, justificar su elección y modificar la opción alternativa para convertirla en correcta. Los resultados menos adecuados corresponden a las dos últimas dimensiones citadas.In this paper we analyse the performance of 8th, 9th and 10th grade students (14, 15 and 16 years old respectively), attending Physics and Chemistry lessons, when assessing the design of scientific research on a precipitation problem identified in the dairy industry. Students' performances are examined separately for each dimension involved in the design: identifying the issue to be studied, posing the hypotheses, planning the research and selecting the ending criterion. For the analysis, we collect participants' individual proposals, which have to include the following tasks: selecting the best option, justifying their choice and modifying the alternative option so that it will be correct. The less adequate results correspond to the last two dimensions

TWO PITUITARY ADENOMAS IN MEN 1

The clinical and genetic features of a 43-year-old male patient with multiple endocrine neoplasia type 1 were reported. He developed hyperparathyroidism, a GHRH-producing pancreatic tumor, and acromegaly between 1980 and 1983. Because his pituitary gland increased in size even after resecting the GHRH-producing pancreatic tumor, transsphenoidal hypophysectomy was performed six years later. The pituitary contained two histologically-different adenomas composed of somatotroph cells and null cells. Genetic analyses revealed loss of heterozygosity on chromosome 11 in common in the pituitary adenomas, the pancreatic endocrine tumors, and a parathyroid hyperplasia. On the other hand, mutations of ras, p53, Gsα, and Gi2α genes were not found in these tumors. The loss of the tumor suppressor gene on chromosome 11q12-13 was involved in the formation of two pituitary adenomas, two pancreatic endocrine functioning tumors, and a parathyroid hyperplasia in this patient, but the tumorigenic factors in the specific endocrine organs remain to be studied

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

レーザー切削面に対するポリマー酸系レジン接着システムの展開と新規開発

本報告書は、「レーザー切削面に対するポリマー酸系レジン接着システムの展開と新規開発」を基盤研究(B)(2)のテーマとして、前述した研究者達が包括的かつ総合的に3年間にわたって鋭意検討してきた研究成果をまとめたものである。以下に、各年度の研究成果の概要とそれらの統括を記した。また、これらの成果の根拠となった研究を、小テーマ別にまとめて後に一括掲載した。(･･････)【統括】Er:YAGレーザー及びCO2レーザー処理象牙質面の性状変化とレジン系修復材料の接着性等について検討を行った。走査電子顕微鏡(SEM)及び原子間力顕微鏡観察によると、レーザー処理面にはスメア層は認められず、亀裂や層状構造物等の構造欠陥が発生していた。また、サーモグラフによると、いずれのレーザーも200℃以上の熱が発生していた。さらに、エネルギー分散型蛍光X線分析装置、電子線マイクロアナライザ、及び超微小硬度計による分析の結果、表層約30μmにおけるCaとPの濃度の減少並びに硬度の低下が認められた。これらの変化に伴ってコラーゲン線経の破壊された一層や熱による変性層が、マッソントリクロム染色による光学顕微鏡(LM)観察、透過電子顕微鏡(TEM)及びX線光電子分析装置を用いた観察により認められた。一方、レーザー処理面に市販の接着システムを応用し微小引張り試験法により検討したところ、初期接着強さや接着耐久性は有意に低下した。このことは、構造欠陥への引張り応力集中、変性層の発生や象牙質の初性低下によるレジンの浸透性阻害や樹脂含浸層等の機械的強度低下等によるものと考えられた。このような両レーザー処理象牙質面に対し現用の接着システムの適応を目指This study was to investigate 1) the changes of surface characteristics of Er:YAG or CO2 lased dentin and 2) the adhesive properties of resinous materials to the lased dentin. From Scanning Electron Microscopic (SEM) and Atomic Force Microscopic (AFM) study, the smear layer could not be detected on the lased dentin surface, and the structural defects such as micro cracks and stratiform structure were formed. Thermographic analysis exhibited that the laser irradiation generated high heat of temperature value of above 200℃. The analysis of lased dentin using Energy Dispersive X-ray Spectroscopy, Electron Probe X-ray Microanalyser, and Nano-indentation Tester revealed the decrease in hardness and in concentration of Ca and P in the superficial layer of approximately 30 Pm thickness. According to these changes heat-denatured layer and a layer with destroyed dentinal collagen fibers were observed under Light Microscopy (LM), Transmission Electron Microscopy (TEM) and X-ray photoelectron Spectroscopy. Early bond strength and durability of adhesion of the commercial adhesives to the lased dentin were significantly lower than those to the rotary cut dentin in micro-tensile bond test. This might be caused by the concentration of stress to those structural defects, by the inhibition of resin-impregnation due to the denatured layer, or by the deterioration of mechanical properties of the hybrid layer and the lased dentin itself. In order to adapt commercial adhesives to lased dentin, pretreatments for the removal of defects and denatured layer were examined. LM, SEM and TEM study revealed that they could be removed with 30 seconds'phosphoric acid etching followed by 60 seconds'(EnYAG) or 120 seconds'(CO2) sodium hypochlorite treatment. This pretreatment could regain adhesive properties of commercial bond systems equally to those to rotary cut dentin.研究期間:平成10-12年度 ; 研究種目: 基盤研究B2 ; 課題番号:1055717