Effect of Benzene and Ethylbenzene on the Transcription of methyl-\u3cem\u3etert\u3c/em\u3e-butyl Ether Degradation Genes of \u3cem\u3eMethylibium petroleiphilum\u3c/em\u3e PM1

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds’ impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1

Gene \u3cem\u3emdpC\u3c/em\u3e Plays a Regulatory Role in the Methyl-\u3cem\u3etert\u3c/em\u3e-butyl Ether Degradation Pathway of \u3cem\u3eMethylibium petroleiphilum\u3c/em\u3e Strain PM1

Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC−. We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA

Contrast inversion in neutral atom microscopy using atomic cluster beams

This work explores the possibility of atomic cluster beams as a probe for neutral atom microscopy (NAM) measurements. Using a beam of Kr clusters with mean size $\sim$ 10$^4$ atoms/cluster we demonstrate that topographical contrast can be obtained, similar to that in the case of monoatomic beams. Further, using atomically thin films of MoS$_2$ grown on SiO$_2$/Si substrate we show that NAM imaging using Kr clusters is also possible in domains where topographical contrast is not expected. Surprisingly, these images show an inverted contrast pattern when compared to the case of monoatomic beams. We attempt to understand these observations on the basis of angular distributions resulting from cluster-surface scattering. Finally, we discuss the implications of these results towards achieving a high lateral resolution neutral atom microscope using atomic cluster beams.Comment: Main manuscript: 10 pages, 6 figures and Supplementary information: 5 pages, 5 figure

Role of cervical length evaluation with transvaginal ultrasound for prediction of preterm delivery in low risk pregnancy

Background: Preterm birth possess a major health burden to the society due to its long - term morbidity, perinatal mortality and high financial expenditures associated with it. Transvaginal ultrasonographic measurement is an effective and objective way of measuring the cervical length. Cervical length <25 mm is considered as the best cervical parameter with a good predictive accuracy for preterm birth. This study was taken up to study the role of cervical length measurement in predicting preterm labor by Trans vaginal sonography (TVS) and to measure cervical length and follow up cases to study the fetal outcome.Methods: Sagital long-axis view of endocervical canal along the entire length was obtained with high frequency endovaginal probe and the length of cervix from external to the internal os was measured. Atleast three measurements were obtained and the best shortest measurement in millimeters was recorded. Transfundal pressure was applied for 15 seconds and cervical length was obtained again. The cases are followed till delivery and outcome is noted.Results: Out of 134 study group of low risk women, 5.9% women and 50% of the women with short cervical length (<25 mm) had preterm birth. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of our study are 75%, 95.2%, 50%, 98.4%, 94% respectively. Among the 134 newborns, majority of the admissions (14) were due to birth asphyxia followed by meconium aspiration syndrome.Conclusions: TVS is a useful technique in assessing the cervical changes during pregnancy and predicting the preterm birth especially when performed between 16-24 weeks of gestational age could identify all the women having short cervical length along with other changes of cervix

An overview on the Impact of Food Fraud Incidences in Various Countries and its Detection Methods, Assessment Techniques and Preventive Measures

Food fraud is not just a local issue but perhaps a global phenomenon. If the food available in the market are undetected or poorly controlled, this can harm consumer health. Food fraud causes a lack of traceability of supply chains and may eventually be a risk to food safety. The purpose of this paper is to acquaint the various types of food fraud and to evaluate the detection methods in identifying the adulterants. It also addresses the importance of vulnerability assessment of food fraud and key actions required for its prevention. Fighting food fraud will remain a race between the fraudsters and scientists developing new methods to prevent them. The review is unique that it summarized food fraud types, basic and instrument-based detection techniques for adulterants identification and it also focuses on the international governing bodies concerned with food laws and regulations. This study also provides perceptions of the interplay between vulnerability assessment and food fraud prevention

A compact and highly collimated atomic/molecular beam source

We describe the design, characterization and application of a simple, highly collimated and compact atomic/molecular beam source. This source is based on a segmented capillary design, constructed using a syringe needle. Angular width measurements and free molecular flow simulations show that the segmented structure effectively suppresses atoms travelling in off-axis directions, resulting in a narrow beam of Helium atoms having a width of 7 mrad (full width half maximum). We demonstrate an application of this source by using it for monitoring real-time changes in surface coverage on a clean Cu(110) surface exposed to oxygen, by measuring specular reflectivity of the Helium beam generated using this source.Comment: 7 pages, 5 figures, supplementary information (1 figure

Double Perovskite Sr2FeMoO6: A Potential Candidate for Room Temperature Magnetoresistance Device Applications

The family of double perovskites first received attention in the 1960s, but the discovery of low field magnetoresistnace (LFMR) and half metallicity of the Sr2FeMoO6 (SFMO) compound was made by Kobayashi et al. in 1998. A fully spin polarized half-metal SFMO (Tc > 400) with excellent magnetoresistance response relatively at small applied fields and high temperatures makes SFMO an ideal candidate for room temperature spintronics applications. Primarily, most of the research work on double perovskites SFMO has been focused on bulk ceramic samples and aimed to understand their structural, magnetic, and magnetotransport properties, along with correlation among them. A material such as SFMO that exhibits a large decrease in resistivity and magnetically order well above room temperature is necessary for the advancement of spintronic devices. If the bulk properties observed could be reproduced in thin films, industrially produced SFMO-based spintronic devices could become a reality. Therefore, the purpose of this chapter is to present the detailed background and descriptions of the double perovskite Sr2FeMoO6 (SFMO) thin films and heterostructures with main emphasis to improve or achieve room temperature magnetoresistance properties especially for room temperature magnetoresistive device applications

Using Deep RNA Sequencing for the Structural Annotation of the Laccaria Bicolor Mycorrhizal Transcriptome

BACKGROUND: Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure. METHODOLOGY: We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derived from the fungus Laccaria bicolor, which develops a mycorrhizal symbiotic association with the roots of many tree species. Our analysis focused on the subset of 1501 gene models that are differentially expressed in the free living vs. mycorrhizal transcriptome and are expected to be important elements related to carbon metabolism, membrane permeability and transport, and intracellular signaling. Of the set of 1501 gene models, 1439 (96%) successfully generated modified gene models in which all error flags were successfully resolved and the sequences aligned to the genomic sequence. The remaining 4% (62 gene models) either had deviations from transcriptomic data that could not be spanned or generated sequence that did not align to genomic sequence. The outcome of this process is a set of high confidence gene models that can be reliably used for experimental characterization of protein function. CONCLUSIONS: 69% of expressed mycorrhizal JGI "best" gene models deviated from the transcript sequence derived by this method. The transcriptomic sequence enabled correction of a majority of the structural inconsistencies and resulted in a set of validated models for 96% of the mycorrhizal genes. The method described here can be applied to improve gene structural annotation in other species, provided that there is a sequenced genome and a set of gene models

Rhinoscleroma causing upper airway obstruction

Rhinoscleroma is a chronic granulomatous condition of the respiratory tract, and is not uncommon in tropical regions; particularly, Mexico, Central America and the Middle East. A few cases have been reported in North America, primarily involving immigrants from endemic countries. The causative organism is Klebsiella rhinoscleromatis, a Gram-negative coccobacillus. Diagnosis is made on the basis of culture of the organism and the characteristic pathology of Mikulicz cells on light microscopy. The condition primarily affects the upper airway, and frequently presents with nasal discharge, nasal obstruction or frontal facial pain. Despite the term 'rhinoscleroma', there may be involvement of the entire respiratory tract. Although the condition is slowly progressive, its natural course portends extensive destruction. Laryngotracheal involvement occurs in approximately 15% to 80% of cases, but patients rarely present with isolated laryngotracheal disease. In the present paper, a case of rhinoscleroma presenting with symptoms of upper airway obstruction is described. A 56-year-old male pharmacist, originally from Egypt, presented with a two-month history of shortness of breath on exertion. He complained of a foreign-body sensation in his throat with associated wheezing but denied chest pain, cough, hemoptysis or hoarseness. He had not experienced fever, weight loss or night sweats. His past medical history was significant for chronic sinusitis since childhood, characterized by long-standing malodourous secretions, crusting and intermittent nasal blockage. He had seen an otolaryngologist and received a tentative diagnosis of immotile cilia syndrome 12 years before his current presentation, although this diagnosis was not proven by biopsy and he was the natural father of two children. He had both hypertension and hyperlipidemia, and no known family history of respiratory illness or malignancy. He quit smoking six weeks before presentation and had a history of one pack/week for 20 years. On physical examination, he appeared well with no evidence of respiratory distress at rest. His blood pressure was 140/90 mmHg. His trachea was midline and he did not have cervical or supraclavicular adenopathy, cyanosis or clubbing. Examination of his chest revealed symmetric chest expansion with normal breath sounds throughout all lung fields, and specifically, an absence of stridor or wheezing. The remainder of his physical examination was normal. A chest x-ray taken at the time of presentation was normal, with no evidence of a mass or parenchymal disease. He had had an x-ray six years previously which appeared the same. He underwent spirometry and produced a flow-volume loop demonstrating classical features of fixed upper airway obstruction A computed tomography scan of the patient's thorax revealed normal lungs with wall thickening of the proximal trachea and an irregular-appearing endoluminal surface at the level of the thyroid. A subsequent computed tomography scan of the head and neck showed moderate circumferential narrowing of the subglottic larynx and superior trachea, as well as nodular thickening at the level of the inferior cricoid resulting in 50% to 60% endoluminal narrowing The patient underwent bronchoscopy, the findings of which were suggestive of a proximal tracheal tumour involving ©2005 Pulsus Group Inc. All rights reserved CASE REPORT the glottis and subglottis. The patient was referred to an otolaryngologist for evaluation of a potential malignancy. Laryngoscopy confirmed that there was a 3 cm tumour of the tracheal lumen, with evidence of cartilaginous destruction. The mid-and distal trachea were clear, as were the supraglottic and glottic larynx. Endoscopic resection was performed to improve the patient's airway and biopsies were sent for pathology. Pathology revealed a packed mucosal infiltrate of histiocytes admixed with inflammatory cells (mainly plasma cells). Silver methenamine and Gram staining revealed numerous Gram-negative bacilli within the histiocytes. The low-power view of the laryngeal biopsy showed an infiltrate of large, vacuolated histiocytes or Mikulicz cells Culture of the tumour specimen confirmed Klebsiella rhinoscleromatis was the causative organism. The patient was started on ciprofloxacin hydrochloride 500 mg twice a day for six weeks. He remained well after resection with no symptoms of upper airway obstruction. Bronchoscopic follow-up at six months demonstrated no recurrence of disease