Rapid and Efficient Isolation of High-Quality Small RNAs from Recalcitrant Plant Species Rich in Polyphenols and Polysaccharides

PubMed Central

Pu, Jinji; Guo, Jianrong; Fan, Zaifeng

2014-01-01

Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of plant development and gene expression. The acquisition of high-quality small RNAs is the first step in the study of its expression and function analysis, yet the extraction method of small RNAs in recalcitrant plant tissues with various secondary metabolites is not well established, especially for tropical and subtropical plant species rich in polysaccharides and polyphenols. Here, we developed a simple and efficient method for high quality small RNAs extraction from recalcitrant plant species. Prior to RNA isolation, a precursory step with a CTAB-PVPP buffer system could efficiently remove compounds and secondary metabolites interfering with RNAs from homogenized lysates. Then, total RNAs were extracted by Trizol reagents followed by a differential precipitation of high-molecular-weight (HMW) RNAs using polyethylene glycol (PEG) 8000. Finally, small RNAs could be easily recovered from supernatant by ethanol precipitation without extra elimination steps. The isolated small RNAs from papaya showed high quality through a clear background on gel and a distinct northern blotting signal with miR159a probe, compared with other published protocols. Additionally, the small RNAs extracted from papaya were successfully used for validation of both predicted miRNAs and the putative conserved tasiARFs. Furthermore, the extraction method described here was also tested with several other subtropical and tropical plant tissues. The purity of the isolated small RNAs was sufficient for such applications as end-point stem-loop RT-PCR and northern blotting analysis, respectively. The simple and feasible extraction method reported here is expected to have excellent potential for isolation of small RNAs from recalcitrant plant tissues rich in polyphenols and polysaccharides. PMID:24787387

A rapid silica spin column-based method of RNA extraction from fruit trees for RT-PCR detection of viruses.

PubMed

Yang, Fan; Wang, Guoping; Xu, Wenxing; Hong, Ni

2017-09-01

Efficient recovery of high quality RNA is very important for successful RT-PCR detection of plant RNA viruses. High levels of polyphenols and polysaccharides in plant tissues can irreversibly bind to and/or co-precipitate with RNA, which influences RNA isolation. In this study, a silica spin column-based RNA isolation method was developed by using commercially available silica columns combined with the application of a tissue lysis solution, and binding and washing buffers with high concentration guanidinium thiocyanate (GuSCN, 50% w/v), which helps remove plant proteins, polysaccharides and polyphenolic compounds. The method was successfully used to extract high quality RNA from citrus (Citrus aurantifolia), grapevine (Vitis vinifera), peach (Prunus persica), pear (Pyrus spp.), taro (Colocosia esculenta) and tobacco (Nicotiana benthamiana) samples. The method was comparable to conventional CTAB method in RNA isolation efficiency, but it was more sample-adaptable and cost-effective than commercial kits. High quality RNA isolated using silica spin column-based method was successfully used for the RT-PCR and/or multiplex RT-PCR amplification of woody fruit tree viruses and a viroid. The study provided a useful tool for the detection and characterization of plant viruses. Copyright © 2017 Elsevier B.V. All rights reserved.

Does High School Facility Quality Affect Student Achievement? A Two-Level Hierarchical Linear Model

ERIC Educational Resources Information Center

Bowers, Alex J.; Urick, Angela

2011-01-01

The purpose of this study is to isolate the independent effects of high school facility quality on student achievement using a large, nationally representative U.S. database of student achievement and school facility quality. Prior research on linking school facility quality to student achievement has been mixed. Studies that relate overall…

Application of in situ ductal perfusion to facilitate isolation of high-quality RNA from mouse pancreas.

PubMed

Mullin, Anne E; Soukatcheva, Galina; Verchere, C Bruce; Chantler, Janet K

2006-05-01

A technique to isolate high-quality intact RNA from murine pancreas is described. This technique involves in situ ductal perfusion of the pancreas with an RNase inhibitor prior to removal of the organ for RNA extraction. In this way, the pancreatic RNases are inhibited in situ allowing good yields of intact RNA, suitable for studies on pancreatic gene transcription by real-time PCR or microarray analysis, to be obtained in a reliable way.

A modified protocol for RNA extraction from different peach tissues suitable for gene isolation and real-time PCR analysis.

PubMed

Tong, Zhaoguo; Qu, Shenchun; Zhang, Jiyu; Wang, Fei; Tao, Jianmin; Gao, Zhihong; Zhang, Zhen

2012-03-01

RNA extraction is the first step in the study of gene isolation and expression. However, it is difficult to extract high quantity and quality RNA from tissues containing large quantities of polysaccharides and polyphenols. Peach (Prunus persica), in addition to containing high levels of polysaccharides and polyphenols, is a challenging starting material for RNA isolation using a single method because of different amounts of those substances in diverse tissues. Based on three reported methods, we developed a modified RNA isolation protocol to solve this problem, leading to high quality and quantity of total RNA from peach mesocarp tissues of fruits which were sampled from all developmental stages and different storage periods, as well as from other tissues including flowers, leaves, stems, and roots. With our modified method, 28-650 μg of total RNA was routinely obtained from per gram of fresh material, gave at least a 1.16-fold improvement by compared with those isolated by other seven methods. The RNA extracts were successfully used in downstream applications such as RT-PCR, RACE, and real-time PCR.

Evaluations of methods for the isolation of high quality RNA from bovine and cervine hide biopsies for use in gene expression studies

USDA-ARS?s Scientific Manuscript database

Molecular investigations of the ruminant response to ectoparasites at the parasite-host interface are critically dependent upon the quality of RNA. The complexity of ruminant skin decreases the capacity to obtain high quality RNA from biopsy samples, which directly affects the reliability of data pr...

Growing vertical ZnO nanorod arrays within graphite: efficient isolation of large size and high quality single-layer graphene.

PubMed

Ding, Ling; E, Yifeng; Fan, Louzhen; Yang, Shihe

2013-07-18

We report a unique strategy for efficiently exfoliating large size and high quality single-layer graphene directly from graphite into DMF dispersions by growing ZnO nanorod arrays between the graphene layers in graphite.

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA

PubMed Central

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells. PMID:29535635

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA.

PubMed

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells.

Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas.

PubMed

Butler, Alexandra E; Matveyenko, Aleksey V; Kirakossian, David; Park, Johanna; Gurlo, Tatyana; Butler, Peter C

Laser capture microdissection (LCM) is a powerful method to isolate specific populations of cells for subsequent analysis such as gene expression profiling, for example, microarrays or ribonucleic (RNA)-Seq. This technique has been applied to frozen as well as formalin-fixed, paraffin-embedded (FFPE) specimens with variable outcomes regarding quality and quantity of extracted RNA. The goal of the study was to develop the methods to isolate high-quality RNA from islets of Langerhans and pancreatic duct glands (PDG) isolated by LCM. We report an optimized protocol for frozen sections to minimize RNA degradation and maximize recovery of expected transcripts from the samples using quantitative real-time polymerase chain reaction (RT-PCR) by adding RNase inhibitors at multiple steps during the experiment. This technique reproducibly delivered intact RNA (RIN values 6-7). Using quantitative RT-PCR, the expected profiles of insulin, glucagon, mucin6 (Muc6), and cytokeratin-19 (CK-19) mRNA in PDGs and pancreatic islets were detected. The described experimental protocol for frozen pancreas tissue might also be useful for other tissues with moderate to high levels of intrinsic ribonuclease (RNase) activity.

RNA isolation from loquat and other recalcitrant woody plants with high quality and yield.

PubMed

Morante-Carriel, Jaime; Sellés-Marchart, Susana; Martínez-Márquez, Ascensión; Martínez-Esteso, María José; Luque, Ignacio; Bru-Martínez, Roque

2014-05-01

RNA isolation is difficult in plants that contain large amounts of polysaccharides and polyphenol compounds. To date, no commercial kit has been developed for the isolation of high-quality RNA from tissues with these characteristics, especially for fruit. The common protocols for RNA isolation are tedious and usually result in poor yields when applied to recalcitrant plant tissues. Here an efficient RNA isolation protocol based on cetyltrimethylammonium bromide (CTAB) and two successive precipitations with 10 M lithium chloride (LiCl) was developed specifically for loquat fruits, but it was proved to work efficiently in other tissues of loquat and woody plants. The RNA isolated by this improved protocol was not only of high purity and integrity (A260/A280 ratios ranged from 1.90 to 2.04 and A260/A230 ratios were>2.0) but also of high yield (up to 720 μg on average [coefficient of variation=21%] total RNA per gram fresh tissue). The protocol was tested on loquat fruit (different stages of development, postharvest, ripening, and bruising), leaf, root, flower, stem, and bud; quince fruit and root; grapevine cells in liquid culture; and rose petals. The RNA obtained with this method is amenable to enzymatic treatments and can be efficiently applied for research on gene characterization, expression, and function. Copyright © 2014 Elsevier Inc. All rights reserved.

Activated charcoal-mediated RNA extraction method for Azadirachta indica and plants highly rich in polyphenolics, polysaccharides and other complex secondary compounds

PubMed Central

2013-01-01

Background High quality RNA is a primary requisite for numerous molecular biological applications but is difficult to isolate from several plants rich in polysaccharides, polyphenolics and other secondary metabolites. These compounds either bind with nucleic acids or often co-precipitate at the final step and many times cannot be removed by conventional methods and kits. Addition of vinyl-pyrollidone polymers in extraction buffer efficiently removes polyphenolics to some extent, but, it failed in case of Azadirachta indica and several other medicinal and aromatic plants. Findings Here we report the use of adsorption property of activated charcoal (0.03%–0.1%) in RNA isolation procedures to remove complex secondary metabolites and polyphenolics to yield good quality RNA from Azadirachta indica. We tested and validated our modified RNA isolation method across 21 different plants including Andrographis paniculata, Aloe vera, Rosa damascena, Pelargonium graveolens, Phyllanthus amarus etc. from 13 other different families, many of which are considered as tough system for isolating RNA. The A260/280 ratio of the extracted RNA ranged between 1.8-2.0 and distinct 28S and 18S ribosomal RNA bands were observed in denaturing agarose gel electrophoresis. Analysis using Agilent 2100 Bioanalyzer revealed intact total RNA yield with very good RNA Integrity Number. Conclusions The RNA isolated by our modified method was found to be of high quality and amenable for sensitive downstream molecular applications like subtractive library construction and RT-PCR. This modified RNA isolation procedure would aid and accelerate the biotechnological studies in complex medicinal and aromatic plants which are extremely rich in secondary metabolic compounds. PMID:23537338

Stress, health and quality of life of female migrant domestic workers in Singapore: a cross-sectional study.

PubMed

Anjara, S G; Nellums, L B; Bonetto, C; Van Bortel, T

2017-10-10

There is a global increase in migrant workers. In Singapore, there are over 230,000 migrant domestic workers (MDWs). Female MDWs may experience high levels of stress and social isolation, which may negatively impact on their health and quality of life. There have also been documented cases of abuse and exploitation. However, there is a lack of empirical research with this population. This study aimed to investigate factors impacting on the health and quality of life of female MDWs in Singapore, including socio-demographic and job related characteristics, stress, social isolation, and working management style. A cross-sectional survey was carried out with 182 female MDWs in Singapore. The survey examined health and quality of life (WHOQoL-Bréf), social connectedness (the Friendship Scale), and preferred and experienced working management style (the Theory X and Theory Y Questionnaire). Descriptive analyses were carried out in addition to ANOVA, t-tests, and chi-square tests, followed by a multivariate analysis using linear regression. Participants were found to have good overall quality of life and satisfaction with health. Age and working experience were found to be significantly (p < 0.05) associated with overall quality of life and three domains (psychological, social, and environmental health). Agreement between experienced and preferred working management style was also found to be associated with higher quality of life scores (with the exception of the social relationships domain). Though women reported relatively good overall quality of life, more than half of participants reported feeling stressed. In addition, nearly 20% of participants reported being isolated or very isolated. Stress was identified to be associated with isolation. In the multivariate analysis, stress was found to contribute to worse quality of life in all domains except social relationships, after adjusting for confounders. Social connectedness was positively associated with all domains of quality of life, and agreement of working management style was positively associated with physical health, psychological health and environmental quality of life. The findings serve as an evidence-base pointing to the need for policies aimed at decreasing stress and social isolation among female MDWs in order to improve their health and quality of life.

High-quality genome of the peach scab pathogen, Venturia carpophila

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia. The genome was sequenced by MiSeq using an Illumina paired-end lib...

Choices and Challenges: Charter School Performance in Perspective

ERIC Educational Resources Information Center

Wohlstetter, Priscilla; Smith, Joanna; Farrell, Caitlin C.

2013-01-01

As charter schools enter their third decade, research in this key sector remains overwhelmingly contradictory and confused. Many studies are narrowly focused; some do not meet the standards for high-quality academic research. In this definitive work, Wohlstetter and her colleagues isolate and distill the high-quality research on charter schools to…

Comparison of two DNA extraction protocols from leave samples of Cotinus coggygria, Citrus sinensis and Genus juglans.

PubMed

Fallah, F; Minaei Chenar, H; Amiri, H; Omodipour, S; Shirbande Ghods, F; Kahrizi, D; Sohrabi, M; Ghorbani, T; Kazemi, E

2017-02-28

High quality DNA is essential for molecular research. Secondary metabolites can affect the quantity and quality DNA. In current research two DNA isolation methods including CTAB and Delaporta (protocols 1 & 2 respectively) were applied in three leave samples from Cotinus coggygria, Citrus sinensis and Genus juglans that their leaves are rich of secondary metabolites. We successfully isolated DNA from C. coggygria, C. sinensis and Genus Juglans using the two protocols described above. Good quality DNA was isolated from C. coggygria, C. sinensis and Genus Juglans using protocol 1, while protocol 2 failed to produce usable DNA from these sources. The highest amount of DNA (1.3-1.6) was obtained from them using protocol 1. As we discovered, procedure 1 may work better for plants with secondary metabolites.

Using Technology to Address Barriers in Rural Special Education for Students with Autism: A Do-It-Yourself Guide

ERIC Educational Resources Information Center

McKissick, Bethany R.; Diegelmann, Karen M.; Parker, Sarah

2017-01-01

Providing high-quality special education services in rural settings has a variety of challenges such as geographic isolation and a lack of resources. One particularly challenging aspect of rural special education is providing general curriculum access. Computer-assisted instruction is one way to provide high-quality specialized instruction that…

Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples.

PubMed

Wimmer, Isabella; Tröscher, Anna R; Brunner, Florian; Rubino, Stephen J; Bien, Christian G; Weiner, Howard L; Lassmann, Hans; Bauer, Jan

2018-04-20

Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable. During RNA isolation, extending tissue lysis time to 10 hours reduced high-molecular-weight species, while additional incubation at 70 °C markedly increased RNA yields. Since FF- and FFPE-derived microarrays constitute different data entities, we used indirect measures to investigate gene signal variation and relative gene expression. Whole-genome analyses revealed high concordance rates, while reviewing on single-genes basis showed higher data variation in FFPE than FF arrays. Using an experimental model, gene set enrichment analysis (GSEA) of FFPE-derived microarrays and fresh tissue-derived RNA-Seq datasets yielded similarly affected pathways confirming the applicability of FFPE tissue in global gene expression analysis. Our study provides a workflow comprising RNA isolation, quality assessment and microarray profiling using minimal RNA input, thus enabling hypothesis-generating pathway analyses from limited amounts of precious, pathologically significant FFPE tissues.

An optimized high quality male DNA extraction from spermatophores in open thelycum shrimp species.

PubMed

Planella, Laia; Heras, Sandra; Vera, Manuel; García-Marín, José-Luis; Roldán, María Inés

2017-09-01

The crucial step of most of the current genetic studies is the extraction of DNA of sufficient quantity and quality. Several genomic DNA isolation methods have been described to successfully obtain male DNA from shrimp species. However, all current protocols require invasive handling methods with males for DNA isolation. Using Aristeus antennatus as a model we tested a reliable non-invasive differential DNA extraction method to male DNA isolation from spermatophores attached to female thelycum. The present protocol provides high quality and quantity DNA for polymerase chain reaction amplification and male genotyping. This new approach could be useful to experimental shrimp culture to select sires with relevant genetic patterns for selective breeding programs. More importantly, it can be applied to identify the mating pairs and male structure in wild populations of species as A. antennatus, where males are often difficult to capture. Our method could be also valuable for biological studies on other spermatophore-using species, such as myriapods, arachnids and insects. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Improving quality and digestibility of cocoa pod with white rot fungi

NASA Astrophysics Data System (ADS)

Mustabi, J.; Wedawati; Armayanti, A. K.

2018-05-01

White rot fungi is a type of fungus that is able to degrade lignin in the feed material from waste, so it can be used to increase the added value of cocoa pod as alternative feed ingredients to meet the nutritional needs of cattle. The purpose of this study is to investigate the use of white rot fungi in improving the quality and digestibility cocoa pod as feed. The study consisted of two phases, namely fermentation using three isolates of white rot fungi (Coprinus comatus, Corilopsis polyzona and Lentinus torulosus) on pod husks and quality testing in vitro digestibility of fermented. Results of analysis of variance show that the treatment was highly significant on the content of lignin, cellulose and hemicellulose pod husks. Fermented cocoa husks with white rot fungi can degrade lignin content of 1.42% - 12.28% and highly significant improved on in vitro digestibility of dry matter and organic matter. The conclusion, isolates of white rot fungi most active in degrading lignin was Lentinus torulosus isolates and less ability to degrade cellulose and hemicellulose.

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Louati, Moussa

Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content and 7,307 predicted protein-coding genes.

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

DOE PAGES

Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Louati, Moussa; ...

2016-08-04

Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content and 7,307 predicted protein-coding genes.

Comparative Analysis of Extended-Spectrum-β-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States

PubMed Central

Folster, Jason P.; Hsu, Chih-Hao; Chen, Jessica; Hoffmann, Maria; Li, Cong; Morales, Cesar; Tyson, Gregory H.; Mukherjee, Sampa; Brown, Allison C.; Green, Alice; Wilson, Wanda; Dessai, Uday; Abbott, Jason; Joseph, Lavin; Haro, Jovita; Ayers, Sherry; McDermott, Patrick F.; Zhao, Shaohua

2017-01-01

ABSTRACT We sequenced the genomes of 10 Salmonella enterica serovar Infantis isolates containing blaCTX-M-65 obtained from chicken, cattle, and human sources collected between 2012 and 2015 in the United States through routine National Antimicrobial Resistance Monitoring System (NARMS) surveillance and product sampling programs. We also completely assembled the plasmids from four of the isolates. All isolates had a D87Y mutation in the gyrA gene and harbored between 7 and 10 resistance genes [aph(4)-Ia, aac(3)-IVa, aph(3′)-Ic, blaCTX-M-65, fosA3, floR, dfrA14, sul1, tetA, aadA1] located in two distinct sites of a megaplasmid (∼316 to 323 kb) similar to that described in a blaCTX-M-65-positive S. Infantis isolate from a patient in Italy. High-quality single nucleotide polymorphism (hqSNP) analysis revealed that all U.S. isolates were closely related, separated by only 1 to 38 pairwise high-quality SNPs, indicating a high likelihood that strains from humans, chickens, and cattle recently evolved from a common ancestor. The U.S. isolates were genetically similar to the blaCTX-M-65-positive S. Infantis isolate from Italy, with a separation of 34 to 47 SNPs. This is the first report of the blaCTX-M-65 gene and the pESI (plasmid for emerging S. Infantis)-like megaplasmid from S. Infantis in the United States, and it illustrates the importance of applying a global One Health human and animal perspective to combat antimicrobial resistance. PMID:28483962

Comparative Analysis of Extended-Spectrum-β-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States.

PubMed

Tate, Heather; Folster, Jason P; Hsu, Chih-Hao; Chen, Jessica; Hoffmann, Maria; Li, Cong; Morales, Cesar; Tyson, Gregory H; Mukherjee, Sampa; Brown, Allison C; Green, Alice; Wilson, Wanda; Dessai, Uday; Abbott, Jason; Joseph, Lavin; Haro, Jovita; Ayers, Sherry; McDermott, Patrick F; Zhao, Shaohua

2017-07-01

We sequenced the genomes of 10 Salmonella enterica serovar Infantis isolates containing bla CTX-M-65 obtained from chicken, cattle, and human sources collected between 2012 and 2015 in the United States through routine National Antimicrobial Resistance Monitoring System (NARMS) surveillance and product sampling programs. We also completely assembled the plasmids from four of the isolates. All isolates had a D87Y mutation in the gyrA gene and harbored between 7 and 10 resistance genes [ aph(4)-Ia , aac(3)-IVa , aph(3 ' )-Ic , bla CTX-M-65 , fosA3 , floR , dfrA14 , sul1 , tetA , aadA1 ] located in two distinct sites of a megaplasmid (∼316 to 323 kb) similar to that described in a bla CTX-M-65 -positive S Infantis isolate from a patient in Italy. High-quality single nucleotide polymorphism (hqSNP) analysis revealed that all U.S. isolates were closely related, separated by only 1 to 38 pairwise high-quality SNPs, indicating a high likelihood that strains from humans, chickens, and cattle recently evolved from a common ancestor. The U.S. isolates were genetically similar to the bla CTX-M-65 -positive S Infantis isolate from Italy, with a separation of 34 to 47 SNPs. This is the first report of the bla CTX-M-65 gene and the pESI (plasmid for emerging S Infantis)-like megaplasmid from S Infantis in the United States, and it illustrates the importance of applying a global One Health human and animal perspective to combat antimicrobial resistance. Copyright © 2017 American Society for Microbiology.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Emmert-Buck, Michael R

2005-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of pancreatic malignancy and other biological phenomena. This chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed-over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification. High-quality tissue microdissection does not necessarily mean high-quality samples to analyze. The quality of biomaterials obtained for analysis is highly dependent on steps upstream and downstream from tissue microdissection. We provide protocols for each of these steps, and encourage you to improve upon these. It is worth the effort of every laboratory to optimize and document its technique at each stage of the process, and we provide a starting point for those willing to spend the time to optimize. In our view, poor documentation of tissue and cell type of origin and the use of nonoptimized protocols is a source of inefficiency in current life science research. Even incremental improvement in this area will increase productivity significantly.

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR ISOLATION OF MALFUNCTIONING OR DAMAGED EQUIPMENT (UA-G-2.0)

EPA Science Inventory

The purpose of this SOP is to identify and isolate malfunctioning or damaged equipment for the NHEXAS Arizona research project. This procedure was followed to ensure consistent data custody, storage, transfer and analysis of a high quality during the Arizona NHEXAS project and t...

Draft Genome sequence of Frankia sp. Strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sen, Arnab; Beauchemin, Nicholas; Bruce, David

Members of actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a high-quality draft genome sequence for Frankia sp. stain QA3, a nitrogen-fixing actinobacterium isolated from root nodules of Alnus nitida.

A simple method of DNA isolation from jute (Corchorus olitorius) seed suitable for PCR-based detection of the pathogen Macrophomina phaseolina (Tassi) Goid.

PubMed

Biswas, C; Dey, P; Satpathy, S; Sarkar, S K; Bera, A; Mahapatra, B S

2013-02-01

A simple method was developed for isolating DNA from jute seed, which contains high amounts of mucilage and secondary metabolites, and a PCR protocol was standardized for detecting the seedborne pathogen Macrophomina phaseolina. The cetyl trimethyl ammonium bromide method was modified with increased salt concentration and a simple sodium acetate treatment to extract genomic as well as fungal DNA directly from infected jute seed. The Miniprep was evaluated along with five other methods of DNA isolation in terms of yield and quality of DNA and number of PCR positive samples. The Miniprep consistently recovered high amounts of DNA with good spectral qualities at A260/A280. The DNA isolated from jute seed was found suitable for PCR amplification. Macrophomina phaseolina could be detected by PCR from artificially inoculated as well as naturally infected jute seeds. The limit of PCR-based detection of M. phaseolina in jute seed was determined to be 0·62 × 10(-7) CFU g(-1) seed. © 2012 The Society for Applied Microbiology.

[Progress in isolation and purification of porcine islets].

PubMed

Zhu, Haitao; Yu, Liang; Wang, Bo

2012-08-01

To review the common methods of isolation and purification of porcine islets and research progress. Domestic and abroad literature concerning the isolation and purification of porcine islets was reviewed and analyzed thoroughly. The efficacy of the isolation and purification depends on the selection of donor, the procurement and cryopreservation of high-quality donor pancreas, and the selection and improvement of the operation. The shortage of transplanted islets could be resolved by the establishment of standardized and optimal process, which may also promote the development of porcine islet xenograft.

Isolating and evaluating lactic acid bacteria strains for effectiveness of Leymus chinensis silage fermentation.

PubMed

Zhang, Q; Li, X J; Zhao, M M; Yu, Z

2014-10-01

Five LAB strains were evaluated using the acid production ability test, morphological observation, Gram staining, physiological, biochemical and acid tolerance tests. All five strains (LP1, LP2, LP3, LC1 and LC2) grew at pH 4·0, and LP1 grew at 15°C. Strains LP1, LP2 and LP3 were identified as Lactobacillus plantarum, whereas LC1 and LC2 were classified as Lactobacillus casei by sequencing 16S rDNA. The five isolated strains and two commercial inoculants (PS and CL) were added to native grass and Leymus chinensis (Trin.) Tzvel. for ensiling. All five isolated strains decreased the pH and ammonia nitrogen content, increased the lactic acid content and LP1, LP2 and LP3 increased the acetic content and lactic/acetic acid ratio of L. chinensis silage significantly. The five isolated strains and two commercial inoculants decreased the butyric acid content of the native grass silage. LP2 treatment had lower butyric acid content and ammonia nitrogen content than the other treatments. The five isolated strains improved the quality of L. chinensis silage. The five isolated strains and the two commercial inoculants were not effective in improving the fermentation quality of the native grass silage, but LP2 performed better comparatively. Significance and impact of the study: Leymus chinensis is an important grass in China and Russia, being the primary grass of the short grassland 'steppe' regions of central Asia. However, it has been difficult to make high-quality silage of this species because of low concentration of water-soluble carbohydrates (WSC). Isolating and evaluating lactic acid bacteria strains will be helpful for improving the silage quality of this extensively grown species. © 2014 The Society for Applied Microbiology.

A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability.

PubMed

Wang, Qi; Hou, Yubin; Wang, Junting; Lu, Qingyou

2013-11-01

We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR ISOLATION OF MALFUNCTIONING OR DAMAGED EQUIPMENT (UA-G-2.0)

EPA Science Inventory

The purpose of this SOP is to identify and isolate malfunctioning or damaged equipment for the Arizona Border Study. This procedure was followed to ensure consistent data custody, storage, transfer and analysis of a high quality during the Arizona NHEXAS project and the Border s...

Collaborative Online Professional Development for Teachers in Higher Education

ERIC Educational Resources Information Center

Teräs, Hanna

2016-01-01

Enhancing teaching quality has become a priority for many universities. The need for high-quality professional development for university teachers is therefore crucial. Earlier research has indicated that isolated workshops often fail to result in significant changes in teaching practice. It has been suggested that the desired transformation…

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis.

PubMed

Peeters, M; Huang, C L; Vonk, L A; Lu, Z F; Bank, R A; Helder, M N; Doulabi, B Zandieh

2016-11-01

Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised.Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560-568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. © 2016 Peeters et al.

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis

PubMed Central

Peeters, M.; Huang, C. L.; Vonk, L. A.; Lu, Z. F.; Bank, R. A.; Doulabi, B. Zandieh

2016-01-01

Objectives Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Materials and Methods Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. Results No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. Conclusion For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised. Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560–568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. PMID:27881439

Novel method for the rapid isolation of RPE cells specifically for RNA extraction and analysis

PubMed Central

Wang, Cynthia Xin-Zhao; Zhang, Kaiyan; Aredo, Bogale; Lu, Hua; Ufret-Vincenty, Rafael L.

2012-01-01

RPE cells are involved in the pathogenesis of many retinal diseases. Accurate analysis of RPE gene expression profiles in different scenarios will increase our understanding of disease mechanisms. Our objective in this study was to develop an improved method for the isolation of RPE cells, specifically for RNA analysis. Mouse RPE cells were isolated using different techniques, including mechanical dissociation techniques and a new technique we refer to here as “Simultaneous RPE cell Isolation and RNA Stabilization” (SRIRS method). RNA was extracted from the RPE cells. An RNA bioanalyzer was used to determine the quantity and quality of RNA. qPCR was used to determine contamination with non-RPE-derived RNA. Several parameters with a potential impact on the isolation protocol were studied and optimized. A marked improvement in the quantity and quality of RPE-derived RNA was obtained with the SRIRS technique. We could get the RPE in direct contact with the RNA protecting agent within 1 minute of enucleation, and the RPE isolated within 11 minutes of enucleation. There was no significant contamination with vascular, choroidal or scleral-derived RNA. We have developed a fast, easy and reliable method for the isolation of RPE cells that leads to a high yield of RPE-derived RNA while preserving its quality. We believe this technique will be useful for future studies looking at gene expression profiles of RPE cells and their role in the pathophysiology of retinal diseases. PMID:22721721

Improved High-Quality Draft Genome Sequence and Annotation of Burkholderia contaminans LMG 23361T.

PubMed

Jung, Ji Young; Ahn, Youngbeom; Kweon, Ohgew; LiPuma, John J; Hussong, David; Marasa, Bernard S; Cerniglia, Carl E

2017-04-20

Burkholderia contaminans LMG 23361 is the type strain of the species isolated from the milk of a dairy sheep with mastitis. Some pharmaceutical products contain disinfectants such as benzalkonium chloride (BZK) and previously we reported that B. contaminans LMG 23361 T possesses the ability to inactivate BZK with high biodegradation rates. Here, we report an improved high-quality draft genome sequence of this strain. Copyright © 2017 Jung et al.

Experimental demonstration of 1.5Hz passive isolation system for precision optical payloads

NASA Astrophysics Data System (ADS)

Guan, Xin; Wang, Guang-yuan; Cao, Dong-jing; Tang, Shao-fan; Chen, Xiang; Liang, Lu; Zheng, Gang-tie

2017-11-01

The ground resolution of remote sensing satellite has been raised from hundreds of meters to less than one meter in recent few decades. As a result, the precision optical payload becomes more and more sensitive to structure vibrations of satellite buses. Although these vibrations generally have extremely low magnitude, they can result in significant image quality degradation to an optical payload. The suggestion of using vibration isolators to isolate payload from the satellite bus has been put forward in 1980s'[1]. Recently, WorldView-2 achieved its perfect image quality via using a set of low frequency isolators[2]. Recently, some of the optical payload manufacturers begin to provide vibration isolators as standard parts together with their main products . During the prototype testing of an earth resource satellite, the image of the optical payload was found to jitter for 5 10 pixels due to disturbances transmitted from the satellite bus structure. Test results indicated that the acceleration level of the vibration was of mG magnitude. To solve the problem, a highly sensitive vibration isolation system was developed to reduce the transmission of disturbances. Integrated isolation performance tests showed that the image jitter can be decreased to below 0.3 pixels.

Method Optimization for Extracting High-Quality RNA From the Human Pancreas Tissue.

PubMed

Jun, Eunsung; Oh, Juyun; Lee, Song; Jun, Hye-Ryeong; Seo, Eun Hye; Jang, Jin-Young; Kim, Song Cheol

2018-06-01

Nucleic acid sequencing is frequently used to determine the molecular basis of diseases. Therefore, proper storage of biological specimens is essential to inhibit nucleic acid degradation. RNA isolated from the human pancreas is generally of poor quality because of its high concentration of endogenous RNase. In this study, we optimized the method for extracting high quality RNA from paired tumor and normal pancreatic tissues obtained from eight pancreatic cancer patients post-surgery. RNA integrity number (RIN) was checked to evaluate the integrity of RNA, we tried to extract the RNA with an RIN value of 8 or higher that allows for the latest genetic analysis. The effect of several parameters, including the method used for tissue lysis, RNAlater treatment, tissue weight at storage, and the time to storage after surgical resection, on the quantity and quality of RNA extracted was examined. Data showed that the highest quantity of RNA was isolated using a combination of manual and mechanical methods of tissue lysis. Additionally, sectioning the tissues into small pieces (<100 mg) and treating them with RNAlater solution prior to storage increased RNA stability. Following these guidelines, high quality RNA was obtained from 100% (8/8) of tumor tissues and 75% (6/8) of normal tissues. High-quality RNA was still stable under repeated freezing and thawing. The application of these results during sample handling and storage in clinical settings will facilitate the genetic diagnosis of diseases and their subsequent treatment. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation.

PubMed

Nohara, Kazunari; Chen, Zheng; Yoo, Seung-Hee

2017-07-06

Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.

The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.

PubMed

Baker, Kate S; Mather, Alison E; McGregor, Hannah; Coupland, Paul; Langridge, Gemma C; Day, Martin; Deheer-Graham, Ana; Parkhill, Julian; Russell, Julie E; Thomson, Nicholas R

2014-11-08

Shigellosis (previously bacillary dysentery) was the primary diarrhoeal disease of World War 1, but outbreaks still occur in military operations, and shigellosis causes hundreds of thousands of deaths per year in developing nations. We aimed to generate a high-quality reference genome of the historical Shigella flexneri isolate NCTC1 and to examine the isolate for resistance to antimicrobials. In this genomic analysis, we sequenced the oldest extant Shigella flexneri serotype 2a isolate using single-molecule real-time (SMRT) sequencing technology. Isolated from a soldier with dysentery from the British forces fighting on the Western Front in World War 1, this bacterium, NCTC1, was the first isolate accessioned into the National Collection of Type Cultures. We created a reference sequence for NCTC1, investigated the isolate for antimicrobial resistance, and undertook comparative genetics with S flexneri reference strains isolated during the 100 years since World War 1. We discovered that NCTC1 belonged to a 2a lineage of S flexneri, with which it shares common characteristics and a large core genome. NCTC1 was resistant to penicillin and erythromycin, and contained a complement of chromosomal antimicrobial resistance genes similar to that of more recent isolates. Genomic islands gained in the S flexneri 2a lineage over time were predominately associated with additional antimicrobial resistances, virulence, and serotype conversion. This S flexneri 2a lineage is a well adapted pathogen that has continued to respond to selective pressures. We have created a valuable historical benchmark for shigellae in the form of a high-quality reference sequence for a publicly available isolate. The Wellcome Trust. Copyright © 2014 Baker et al. Open Access article distributed under the terms of CC BY. Published by Elsevier Ltd. All rights reserved.

Prospective associations of social isolation and loneliness with poor sleep quality in older adults.

PubMed

Yu, Bin; Steptoe, Andrew; Niu, Kaijun; Ku, Po-Wen; Chen, Li-Jung

2018-03-01

There is evidence for negative associations between social isolation and loneliness and sleep quality in older adults. However, it is unclear to what extent these two factors independently affect sleep quality. This study examined the simultaneous associations of social isolation and loneliness with sleep quality in a longitudinal study of older adults. Data were analyzed from the Social Environment and Biomarkers of Aging Study in Taiwan collected in 2000 and 2006, involving a cohort of 639 participants (mean age = 66.14, SD 7.26). Poisson regression models were conducted to examine the association of social isolation and/or loneliness with sleep quality at follow-up after adjusting for multiple confounding variables. Univariate analysis showed that sleep quality was inversely associated with both social isolation and loneliness. After demographic, health, cognitive factors, and depressive symptoms were controlled in multivariable analysis, social isolation at the baseline still predicted poor sleep quality 6 years later (incident rate ratio, IRR 1.14; 95% CI 1.04-1.24; p < 0.01), while the association between loneliness and sleep quality was no longer significant (IRR 1.08; 95% CI 0.94-1.23; p = 0.27). The results were unchanged when participants who had poor sleep quality at the baseline were excluded from the analysis. These findings confirm an adverse effect of social isolation on the sleep quality of older adults, but indicate that this effect is independent of loneliness. Social isolation and loneliness seem to have distinct pathways in affecting the sleep quality of older adults.

A simple, fast, and inexpensive CTAB-PVP-silica based method for genomic DNA isolation from single, small insect larvae and pupae.

PubMed

Huanca-Mamani, W; Rivera-Cabello, D; Maita-Maita, J

2015-07-17

In this study, we report a modified CTAB-PVP method combined with silicon dioxide (silica) treatment for the extraction of high quality genomic DNA from a single larva or pupa. This method efficiently obtains DNA from small specimens, which is difficult and challenging because of the small amount of starting tissue. Maceration with liquid nitrogen, phenol treatment, and the ethanol precipitation step are eliminated using this methodology. The A260/A280 absorbance ratios of the isolated DNA were approximately 1.8, suggesting that the DNA is pure and can be used for further molecular analysis. The quality of the isolated DNA permits molecular applications and represents a fast, cheap, and effective alternative method for laboratories with low budgets.

Thermomyces lanuginosus STm: a source of thermostable hydrolytic enzymes for novel application in extraction of high-quality natural rubber from Taraxacum kok-saghyz (rubber dandelion)

USDA-ARS?s Scientific Manuscript database

Hydrolytic enzymes from a newly isolated strain of the thermophilic fungus Thermomyces lanuginosus were used to extract rubber from Taraxacum kok-saghyz commonly known as rubber (or Russian or Kazak(h)) dandelion. The fungus was isolated from garden soil and identified as Thermomyces lanuginosus STm...

Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rice, Marlen C.; Norton, Jeanette M.; Stein, Lisa Y.

ABSTRACT Nitrosomonas cryotoleransATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO 2 fixation were identified.

High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr

USDA-ARS?s Scientific Manuscript database

Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a ...

Assessing the Role of the Courts in Addressing the Educational Problems Caused by Racial Isolation in School Finance Litigation

ERIC Educational Resources Information Center

Green, Preston C., III.

2013-01-01

Since the separate-but-equal era, students attending schools with high concentrations of Black students have attempted to improve the quality of their educations through school finance litigation. Because of the negative effects of racial isolation, Black students might consider mounting school finance litigation to force states to explicitly…

Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters

DOE PAGES

Rice, Marlen C.; Norton, Jeanette M.; Stein, Lisa Y.; ...

2017-03-16

ABSTRACT Nitrosomonas cryotoleransATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO 2 fixation were identified.

RNA isolation from mammalian cells using porous polymer monoliths: an approach for high-throughput automation.

PubMed

Chatterjee, Anirban; Mirer, Paul L; Zaldivar Santamaria, Elvira; Klapperich, Catherine; Sharon, Andre; Sauer-Budge, Alexis F

2010-06-01

The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species.

PubMed

Liu, Xia; Xu, Yongdong; Li, Zhi; Jiang, Shengwei; Yao, Shuo; Wu, Rina; An, Yingfeng

2018-04-21

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.

Non-conventional approaches to food processing in CELSS. I - Algal proteins: Characterization and process optimization

NASA Technical Reports Server (NTRS)

Nakhost, Z.; Karel, M.; Krukonis, V. J.

1987-01-01

Protein isolate obtained from green algae (Scenedesmus obliquus) cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine makes algal protein isolate a high quality component of CELSS diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical CO2 resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Non-conventional approaches to food processing in CELSS, 1. Algal proteins: Characterization and process optimization

NASA Technical Reports Server (NTRS)

Nakhost, Z.; Karel, M.; Krukonis, V. J.

1987-01-01

Protein isolate obtained from green algae cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine make algal protein isolate a high quality component of closed ecological life support system diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical carbon dioxide resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Characteristics of lactic acid bacteria isolates and their effect on the fermentation quality of Napier grass silage at three high temperatures.

PubMed

Gulfam, Ali; Guo, Gang; Tajebe, Seare; Chen, Lei; Liu, Qinhua; Yuan, Xianjun; Bai, Yunfeng; Saho, Tao

2017-04-01

The poor fermentation quality of silage is an important issue for silage production during the high temperatures of summer. Pediococcus acidilactici GG13 (GG13) and Lactobacillus rhamnosus GG26 (GG26) isolated from Italian ryegrass (Lolium multiflorum Lam.) silage were characterised by morphological and physiological tests and 16S rRNA sequencing analysis, and their effects, along with those of a commercial lactic acid bacteria (LAB) inoculant (CB), on the fermentation quality of facultative halophyte Napier grass (Pennisetum purpureum Schumach) ensiled at 30 °C, 40 °C and 50 °C were studied, respectively. The strains GG13 and GG26 grew well at 50 °C and pH 3.5, and were tolerant to 6.5% NaCl. After ensiling for 50 days, the strains GG13 and GG26 and the CB decreased (P < 0.001) the pH and acetic acid and ammonia-N contents and increased (P < 0.001) the lactic acid contents at 30 °C, and decreased (P < 0.001) the ammonia-N contents at 40 °C in Napier grass. CB did not affect the fermentation quality at 50 °C, whereas both isolated strains improved the fermentation quality of Napier grass silage as indicated by the lower (P < 0.001) pH, butyric acid and ammonia-N contents and higher (P < 0.001) lactic acid contents. The strain GG13 is better than GG26 with regard to improvement in fermentation quality of Napier grass silage. The results of this study suggested that strain GG13 is a good LAB inoculant for producing well-fermented silages during the high temperatures of summer times. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Pancreatic islet isolation variables in non-human primates (rhesus macaques).

PubMed

Andrades, P; Asiedu, C K; Gansuvd, B; Inusah, S; Goodwin, K J; Deckard, L A; Jargal, U; Thomas, J M

2008-07-01

Non-human primates (NHPs) are important preclinical models for pancreatic islet transplantation (PIT) because of their close phylogenetic and immunological relationship with humans. However, low availability of NHP tissue, long learning curves and prohibitive expenses constrain the consistency of isolated NHP islets for PIT studies. To advance preclinical studies, we attempted to identify key variables that consistently influence the quantity and quality of NHP islets. Seventy-two consecutive pancreatic islet isolations from rhesus macaques were reviewed retrospectively. A scaled down, semi-automated islet isolation method was used, and monkeys with streptozotocin-induced diabetes, weighing 3-7 kg, served as recipients for allotransplantation. We analysed the effects of 22 independent variables grouped as donor factors, surgical factors and isolation technique factors. Islet yields, success of isolation and transplantation results were used as quantitative and qualitative outcomes. In the multivariate analysis, variables that significantly affected islet yield were the type of monkey, pancreas preservation, enzyme lot and volume of enzyme delivered. The variables associated with successful isolation were the enzyme lot and volume delivered. The transplant result was correlated with pancreas preservation, enzyme lot, endotoxin levels and COBE collection method. Islet quantity and quality are highly variable between isolations. The data reviewed suggest that future NHP isolations should use bilayer preservation, infuse more than 80 ml of Liberase into the pancreas, collect non-fractioned tissue from the COBE, and strictly monitor for infection.

All-In-One: Advanced preparation of Human Parenchymal and Non-Parenchymal Liver Cells.

PubMed

Werner, Melanie; Driftmann, Sabrina; Kleinehr, Kathrin; Kaiser, Gernot M; Mathé, Zotlan; Treckmann, Juergen-Walter; Paul, Andreas; Skibbe, Kathrin; Timm, Joerg; Canbay, Ali; Gerken, Guido; Schlaak, Joerg F; Broering, Ruth

2015-01-01

Liver cells are key players in innate immunity. Thus, studying primary isolated liver cells is necessary for determining their role in liver physiology and pathophysiology. In particular, the quantity and quality of isolated cells are crucial to their function. Our aim was to isolate a large quantity of high-quality human parenchymal and non-parenchymal cells from a single liver specimen. Hepatocytes, Kupffer cells, liver sinusoidal endothelial cells, and stellate cells were isolated from liver tissues by collagenase perfusion in combination with low-speed centrifugation, density gradient centrifugation, and magnetic-activated cell sorting. The purity and functionality of cultured cell populations were controlled by determining their morphology, discriminative cell marker expression, and functional activity. Cell preparation yielded the following cell counts per gram of liver tissue: 2.0 ± 0.4 × 10(7) hepatocytes, 1.8 ± 0.5 × 10(6 )Kupffer cells, 4.3 ± 1.9 × 10(5) liver sinusoidal endothelial cells, and 3.2 ± 0.5 × 10(5) stellate cells. Hepatocytes were identified by albumin (95.5 ± 1.7%) and exhibited time-dependent activity of cytochrome P450 enzymes. Kupffer cells expressed CD68 (94.5 ± 1.2%) and exhibited phagocytic activity, as determined with 1 μm latex beads. Endothelial cells were CD146(+) (97.8 ± 1.1%) and exhibited efficient uptake of acetylated low-density lipoprotein. Hepatic stellate cells were identified by the expression of α-smooth muscle actin (97.1 ± 1.5%). These cells further exhibited retinol (vitamin A)-mediated autofluorescence. Our isolation procedure for primary parenchymal and non-parenchymal liver cells resulted in cell populations of high purity and quality, with retained physiological functionality in vitro. Thus, this system may provide a valuable tool for determining liver function and disease.

Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.

PubMed

Pérez-Portela, Rocío; Riesgo, Ana

2013-09-01

Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high-quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash-frozen and stored at -80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at -80 °C, RNAlater and storage at -20 °C, preservation in TRIzol reagent and storage at -80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips. © 2013 John Wiley & Sons Ltd.

Adding Value to Goat Meat: Biochemical and Technological Characterization of Autochthonous Lactic Acid Bacteria to Achieve High-Quality Fermented Sausages

PubMed Central

Nediani, Miriam T.; García, Luis; Saavedra, Lucila; Martínez, Sandra; López Alzogaray, Soledad; Fadda, Silvina

2017-01-01

Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product. PMID:28513575

Adding Value to Goat Meat: Biochemical and Technological Characterization of Autochthonous Lactic Acid Bacteria to Achieve High-Quality Fermented Sausages.

PubMed

Nediani, Miriam T; García, Luis; Saavedra, Lucila; Martínez, Sandra; López Alzogaray, Soledad; Fadda, Silvina

2017-05-17

Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product.

The effectiveness of e-Interventions on reducing social isolation in older persons: A systematic review of systematic reviews.

PubMed

Chipps, Jennifer; Jarvis, Mary Ann; Ramlall, Suvira

2017-12-01

As the older adult population group has been increasing in size, there has been evidence of growing social isolation and loneliness in their lives. The increased use of information communication technology and Internet-supported interventions has stimulated an interest in the benefits of e-Interventions for older people and specifically in having a role in increasing social networks and decreasing loneliness. A systematic review of e-Interventions to reduce loneliness in older people was conducted with the aim to synthesize high quality evidence on the effectiveness of e-Interventions to decrease social isolation/loneliness for older people living in community/residential care. A systematic search of 12 databases for reviews published between 2000-2017 was conducted using search term synonyms for older people, social isolation and interventions. Three independent researchers screened articles and two reviewers extracted data. The Revised-Assessment of Multiple Systematic Reviews was used to assess the quality of reviews. The final search identified 12 reviews, which included 22 unique primary research studies evaluating e-Interventions for social isolation or loneliness. The reviews were of moderate quality and the primary studies showed a lack of rigor. Loneliness was most frequently measured using the University California Los Angeles Loneliness Scale. Despite the limitations of the reviewed studies, there is inconsistent and weak evidence on using e-Interventions for loneliness in older people.

Identification of intact high molecular weight glutenin subunits from the wheat proteome using combined liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Lagrain, Bert; Brunnbauer, Markus; Rombouts, Ine; Koehler, Peter

2013-01-01

The present paper describes a method for the identification of intact high molecular weight glutenin subunits (HMW-GS), the quality determining proteins from the wheat storage proteome. The method includes isolation of HMW-GS from wheat flour, further separation of HMW-GS by reversed-phase high-performance liquid chromatography (RP-HPLC), and their subsequent molecular identification with electrospray ionization mass spectrometry using a quadrupole-time-of-flight mass analyzer. For HMW-GS isolation, wheat proteins were reduced and extracted from flour with 50% 1-propanol containing 1% dithiothreitol. HMW-GS were then selectively precipitated from the protein mixture by adjusting the 1-propanol concentration to 60%. The composition of the precipitated proteins was first evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis with Coomassie staining and RP-HPLC with ultraviolet detection. Besides HMW-GS (≥65%), the isolated proteins mainly contained ω5-gliadins. Secondly, the isolated protein fraction was analyzed by liquid chromatography-mass spectrometry. Optimal chromatographic separation of HMW-GS from the other proteins in the isolated fraction was obtained when the mobile phase contained 0.1% trifluoroacetic acid as ion-pairing agent. Individual HMW-GS were then identified by determining their molecular masses from the high-resolution mass spectra and comparing these with theoretical masses calculated from amino acid sequences. Using formic acid instead of trifluoroacetic acid in the mobile phase increased protein peak intensities in the base peak mass chromatogram. This allowed the detection of even traces of other wheat proteins than HMW-GS in the isolated fraction, but the chromatographic separation was inferior with a major overlap between the elution ranges of HMW-GS and ω-gliadins. Overall, the described method allows a rapid assessment of wheat quality through the direct determination of the HMW-GS composition and offers a basis for further top-down proteomics of individual HMW-GS and the entire wheat glutenin fraction.

Identification of Intact High Molecular Weight Glutenin Subunits from the Wheat Proteome Using Combined Liquid Chromatography-Electrospray Ionization Mass Spectrometry

PubMed Central

Lagrain, Bert; Brunnbauer, Markus; Rombouts, Ine; Koehler, Peter

2013-01-01

The present paper describes a method for the identification of intact high molecular weight glutenin subunits (HMW-GS), the quality determining proteins from the wheat storage proteome. The method includes isolation of HMW-GS from wheat flour, further separation of HMW-GS by reversed-phase high-performance liquid chromatography (RP-HPLC), and their subsequent molecular identification with electrospray ionization mass spectrometry using a quadrupole-time-of-flight mass analyzer. For HMW-GS isolation, wheat proteins were reduced and extracted from flour with 50% 1-propanol containing 1% dithiothreitol. HMW-GS were then selectively precipitated from the protein mixture by adjusting the 1-propanol concentration to 60%. The composition of the precipitated proteins was first evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis with Coomassie staining and RP-HPLC with ultraviolet detection. Besides HMW-GS (≥65%), the isolated proteins mainly contained ω5-gliadins. Secondly, the isolated protein fraction was analyzed by liquid chromatography-mass spectrometry. Optimal chromatographic separation of HMW-GS from the other proteins in the isolated fraction was obtained when the mobile phase contained 0.1% trifluoroacetic acid as ion-pairing agent. Individual HMW-GS were then identified by determining their molecular masses from the high-resolution mass spectra and comparing these with theoretical masses calculated from amino acid sequences. Using formic acid instead of trifluoroacetic acid in the mobile phase increased protein peak intensities in the base peak mass chromatogram. This allowed the detection of even traces of other wheat proteins than HMW-GS in the isolated fraction, but the chromatographic separation was inferior with a major overlap between the elution ranges of HMW-GS and ω-gliadins. Overall, the described method allows a rapid assessment of wheat quality through the direct determination of the HMW-GS composition and offers a basis for further top-down proteomics of individual HMW-GS and the entire wheat glutenin fraction. PMID:23520527

Ultra precision machining

NASA Astrophysics Data System (ADS)

Debra, Daniel B.; Hesselink, Lambertus; Binford, Thomas

1990-05-01

There are a number of fields that require or can use to advantage very high precision in machining. For example, further development of high energy lasers and x ray astronomy depend critically on the manufacture of light weight reflecting metal optical components. To fabricate these optical components with machine tools they will be made of metal with mirror quality surface finish. By mirror quality surface finish, it is meant that the dimensions tolerances on the order of 0.02 microns and surface roughness of 0.07. These accuracy targets fall in the category of ultra precision machining. They cannot be achieved by a simple extension of conventional machining processes and techniques. They require single crystal diamond tools, special attention to vibration isolation, special isolation of machine metrology, and on line correction of imperfection in the motion of the machine carriages on their way.

Incidence of Fusarium spp. and Levels of Fumonisin B1 in Maize in Western Kenya

PubMed Central

Kedera, C. J.; Plattner, R. D.; Desjardins, A. E.

1999-01-01

Maize kernel samples were collected in 1996 from smallholder farm storages in the districts of Bomet, Bungoma, Kakamega, Kericho, Kisii, Nandi, Siaya, Trans Nzoia, and Vihiga in the tropical highlands of western Kenya. Two-thirds of the samples were good-quality maize, and one-third were poor-quality maize with a high incidence of visibly diseased kernels. One hundred fifty-three maize samples were assessed for Fusarium infection by culturing kernels on a selective medium. The isolates obtained were identified to the species level based on morphology and on formation of the sexual stage in Gibberella fujikuroi mating population tests. Fusarium moniliforme (G. fujikuroi mating population A) was isolated most frequently, but F. subglutinans (G. fujikuroi mating population E), F. graminearum, F. oxysporum, F. solani, and other Fusarium species were also isolated. The high incidence of kernel infection with the fumonisin-producing species F. moniliforme indicated a potential for fumonisin contamination of Kenyan maize. However, analysis of 197 maize kernel samples by high-performance liquid chromatography found little fumonisin B1 in most of the samples. Forty-seven percent of the samples contained fumonisin B1 at levels above the detection limit (100 ng/g), but only 5% were above 1,000 ng/g, a proposed level of concern for human consumption. The four most-contaminated samples, with fumonisin B1 levels ranging from 3,600 to 11,600 ng/g, were from poor-quality maize collected in the Kisii district. Many samples with a high incidence of visibly diseased kernels contained little or no fumonisin B1, despite the presence of F. moniliforme. This result may be attributable to the inability of F. moniliforme isolates present in Kenyan maize to produce fumonisins, to the presence of other ear rot fungi, and/or to environmental conditions unfavorable for fumonisin production. PMID:9872757

Differences between physician social networks for cardiac surgery serving communities with high versus low proportions of black residents.

PubMed

Hollingsworth, John M; Funk, Russell J; Garrison, Spencer A; Owen-Smith, Jason; Kaufman, Samuel R; Landon, Bruce E; Birkmeyer, John D

2015-02-01

Compared with white patients, black patients are more likely to undergo cardiac surgery at low-quality hospitals, even when they live closer to high-quality ones. Opportunities for organizational interventions to alleviate this problem remain elusive. To explore physician isolation in communities with high proportions of black residents as a factor contributing to racial disparities in access to high-quality hospitals for cardiac surgery. Using national Medicare data (2008-2011), we mapped physician social networks at hospitals where coronary artery bypass grafting procedures were performed, measuring their degree of connectedness. We then fitted a series of multivariate regression models to examine for associations between physician connectedness and the proportion of black residents in the hospital service area (HSA) served by each network. Measures of physician connectedness (ie, repeat-tie fraction, clustering, and number of external ties). After accounting for regional differences in healthcare capacity, the social networks of physicians practicing in areas with more black residents varied in many important respects from those of HSAs with fewer black residents. Physicians serving HSAs with many black residents had a smaller number of repeated interactions with each other than those in other HSAs (P<0.001). When these physicians did interact, they tended to assemble in smaller groups of highly interconnected colleagues (P<0.001). They also had fewer interactions with physicians outside their immediate geographic area (P=0.048). Physicians in HSAs with many black residents are more isolated than those in HSAs with fewer black residents. This isolation may negatively impact on care coordination and information sharing. As such, planned delivery system reforms that encourage minorities to seek care within their established local networks may further exacerbate existing surgical disparities.

A Comparative Study of Serum Exosome Isolation Using Differential Ultracentrifugation and Three Commercial Reagents.

PubMed

Helwa, Inas; Cai, Jingwen; Drewry, Michelle D; Zimmerman, Arthur; Dinkins, Michael B; Khaled, Mariam Lotfy; Seremwe, Mutsa; Dismuke, W Michael; Bieberich, Erhard; Stamer, W Daniel; Hamrick, Mark W; Liu, Yutao

2017-01-01

Exosomes play a role in cell-to-cell signaling and serve as possible biomarkers. Isolating exosomes with reliable quality and substantial concentration is a major challenge. Our purpose is to compare the exosomes extracted by three different exosome isolation kits (miRCURY, ExoQuick, and Invitrogen Total Exosome Isolation Reagent) and differential ultracentrifugation (UC) using six different volumes of a non-cancerous human serum (5 ml, 1 ml, 500 μl, 250 μl, 100 μl, and 50 μl) and three different volumes (1 ml, 500 μl and 100 μl) of six individual commercial serum samples collected from human donors. The smaller starting volumes (100 μl and 50 μl) are used to mimic conditions of limited availability of heterogeneous biological samples. The isolated exosomes were characterized based upon size, quantity, zeta potential, CD63 and CD9 protein expression, and exosomal RNA (exRNA) quality and quantity using several complementary methods: nanoparticle tracking analysis (NTA) with ZetaView, western blot, transmission electron microscopy (TEM), the Agilent Bioanalyzer system, and droplet digital PCR (ddPCR). Our NTA results showed that all isolation techniques produced exosomes within the expected size range (40-150 nm). The three kits, though, produced a significantly higher yield (80-300 fold) of exosomes as compared to UC for all serum volumes, except 5 mL. We also found that exosomes isolated by the different techniques and serum volumes had similar zeta potentials to previous studies. Western blot analysis and TEM immunogold labelling confirmed the expression of two common exosomal protein markers, CD63 and CD9, in samples isolated by all techniques. All exosome isolations yielded high quality exRNA, containing mostly small RNA with a peak between 25 and 200 nucleotides in size. ddPCR results indicated that exosomes isolated from similar serum volumes but different isolation techniques rendered similar concentrations of two selected exRNA: hsa-miR-16 and hsa-miR-451. In summary, the three commercial exosome isolation kits are viable alternatives to UC, even when limited amounts of biological samples are available.

Development of a novel and highly efficient method of isolating bacteriophages from water.

PubMed

Liu, Weili; Li, Chao; Qiu, Zhi-Gang; Jin, Min; Wang, Jing-Feng; Yang, Dong; Xiao, Zhong-Hai; Yuan, Zhao-Kang; Li, Jun-Wen; Xu, Qun-Ying; Shen, Zhi-Qiang

2017-08-01

Bacteriophages are widely used to the treatment of drug-resistant bacteria and the improvement of food safety through bacterial lysis. However, the limited investigations on bacteriophage restrict their further application. In this study, a novel and highly efficient method was developed for isolating bacteriophage from water based on the electropositive silica gel particles (ESPs) method. To optimize the ESPs method, we evaluated the eluent type, flow rate, pH, temperature, and inoculation concentration of bacteriophage using bacteriophage f2. The quantitative detection reported that the recovery of the ESPs method reached over 90%. The qualitative detection demonstrated that the ESPs method effectively isolated 70% of extremely low-concentration bacteriophage (10 0 PFU/100L). Based on the host bacteria composed of 33 standard strains and 10 isolated strains, the bacteriophages in 18 water samples collected from the three sites in the Tianjin Haihe River Basin were isolated by the ESPs and traditional methods. Results showed that the ESPs method was significantly superior to the traditional method. The ESPs method isolated 32 strains of bacteriophage, whereas the traditional method isolated 15 strains. The sample isolation efficiency and bacteriophage isolation efficiency of the ESPs method were 3.28 and 2.13 times higher than those of the traditional method. The developed ESPs method was characterized by high isolation efficiency, efficient handling of large water sample size and low requirement on water quality. Copyright © 2017. Published by Elsevier B.V.

Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding.

PubMed

Román, Belén; González-Verdejo, Clara I; Peña, Francisco; Nadal, Salvador; Gómez, Pedro

2012-01-01

Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent. To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA. Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification. In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols. Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue. Copyright © 2012 John Wiley & Sons, Ltd.

High power, high beam quality regenerative amplifier

DOEpatents

Hackel, L.A.; Dane, C.B.

1993-08-24

A regenerative laser amplifier system generates high peak power and high energy per pulse output beams enabling generation of X-rays used in X-ray lithography for manufacturing integrated circuits. The laser amplifier includes a ring shaped optical path with a limited number of components including a polarizer, a passive 90 degree phase rotator, a plurality of mirrors, a relay telescope, and a gain medium, the components being placed close to the image plane of the relay telescope to reduce diffraction or phase perturbations in order to limit high peak intensity spiking. In the ring, the beam makes two passes through the gain medium for each transit of the optical path to increase the amplifier gain to loss ratio. A beam input into the ring makes two passes around the ring, is diverted into an SBS phase conjugator and proceeds out of the SBS phase conjugator back through the ring in an equal but opposite direction for two passes, further reducing phase perturbations. A master oscillator inputs the beam through an isolation cell (Faraday or Pockels) which transmits the beam into the ring without polarization rotation. The isolation cell rotates polarization only in beams proceeding out of the ring to direct the beams out of the amplifier. The diffraction limited quality of the input beam is preserved in the amplifier so that a high power output beam having nearly the same diffraction limited quality is produced.

High power, high beam quality regenerative amplifier

DOEpatents

Hackel, Lloyd A.; Dane, Clifford B.

1993-01-01

A regenerative laser amplifier system generates high peak power and high energy per pulse output beams enabling generation of X-rays used in X-ray lithography for manufacturing integrated circuits. The laser amplifier includes a ring shaped optical path with a limited number of components including a polarizer, a passive 90 degree phase rotator, a plurality of mirrors, a relay telescope, and a gain medium, the components being placed close to the image plane of the relay telescope to reduce diffraction or phase perturbations in order to limit high peak intensity spiking. In the ring, the beam makes two passes through the gain medium for each transit of the optical path to increase the amplifier gain to loss ratio. A beam input into the ring makes two passes around the ring, is diverted into an SBS phase conjugator and proceeds out of the SBS phase conjugator back through the ring in an equal but opposite direction for two passes, further reducing phase perturbations. A master oscillator inputs the beam through an isolation cell (Faraday or Pockels) which transmits the beam into the ring without polarization rotation. The isolation cell rotates polarization only in beams proceeding out of the ring to direct the beams out of the amplifier. The diffraction limited quality of the input beam is preserved in the amplifier so that a high power output beam having nearly the same diffraction limited quality is produced.

Long-term quality assurance of [(18)F]-fluorodeoxyglucose (FDG) manufacturing.

PubMed

Gaspar, Ludovit; Reich, Michal; Kassai, Zoltan; Macasek, Fedor; Rodrigo, Luis; Kruzliak, Peter; Kovac, Peter

2016-01-01

Nine years of experience with 2286 commercial synthesis allowed us to deliver comprehensive information on the quality of (18)F-FDG production. Semi-automated FDG production line using Cyclone 18/9 machine (IBA Belgium), TRACERLab MXFDG synthesiser (GE Health, USA) using alkalic hydrolysis, grade "A" isolator with dispensing robotic unit (Tema Sinergie, Italy), and automatic control system under GAMP5 (minus2, Slovakia) was assessed by TQM tools as highly reliable aseptic production line, fully compliant with Good Manufacturing Practice and just-in-time delivery of FDG radiopharmaceutical. Fluoride-18 is received in steady yield and of very high radioactive purity. Synthesis yields exhibited high variance connected probably with quality of disposable cassettes and chemicals sets. Most performance non-conformities within the manufacturing cycle occur at mechanical nodes of dispensing unit. The long-term monitoring of 2286 commercial synthesis indicated high reliability of automatic synthesizers. Shewhart chart and ANOVA analysis showed that minor non-compliances occurred were mostly caused by the declinations of less experienced staff from standard operation procedures, and also by quality of automatic cassettes. Only 15 syntheses were found unfinished and in 4 cases the product was out-of-specification of European Pharmacopoeia. Most vulnerable step of manufacturing was dispensing and filling in grade "A" isolator. Its cleanliness and sterility was fully controlled under the investigated period by applying hydrogen peroxide vapours (VHP). Our experience with quality assurance in the production of [(18)F]-fluorodeoxyglucose (FDG) at production facility of BIONT based on TRACERlab MXFDG production module can be used for bench-marking of the emerging manufacturing and automated manufacturing systems.

Long-term quality assurance of [18F]-fluorodeoxyglucose (FDG) manufacturing

PubMed Central

Gaspar, Ludovit; Reich, Michal; Kassai, Zoltan; Macasek, Fedor; Rodrigo, Luis; Kruzliak, Peter; Kovac, Peter

2016-01-01

Nine years of experience with 2286 commercial synthesis allowed us to deliver comprehensive information on the quality of 18F-FDG production. Semi-automated FDG production line using Cyclone 18/9 machine (IBA Belgium), TRACERLab MXFDG synthesiser (GE Health, USA) using alkalic hydrolysis, grade “A” isolator with dispensing robotic unit (Tema Sinergie, Italy), and automatic control system under GAMP5 (minus2, Slovakia) was assessed by TQM tools as highly reliable aseptic production line, fully compliant with Good Manufacturing Practice and just-in-time delivery of FDG radiopharmaceutical. Fluoride-18 is received in steady yield and of very high radioactive purity. Synthesis yields exhibited high variance connected probably with quality of disposable cassettes and chemicals sets. Most performance non-conformities within the manufacturing cycle occur at mechanical nodes of dispensing unit. The long-term monitoring of 2286 commercial synthesis indicated high reliability of automatic synthesizers. Shewhart chart and ANOVA analysis showed that minor non-compliances occurred were mostly caused by the declinations of less experienced staff from standard operation procedures, and also by quality of automatic cassettes. Only 15 syntheses were found unfinished and in 4 cases the product was out-of-specification of European Pharmacopoeia. Most vulnerable step of manufacturing was dispensing and filling in grade “A” isolator. Its cleanliness and sterility was fully controlled under the investigated period by applying hydrogen peroxide vapours (VHP). Our experience with quality assurance in the production of [18F]-fluorodeoxyglucose (FDG) at production facility of BIONT based on TRACERlab MXFDG production module can be used for bench-marking of the emerging manufacturing and automated manufacturing systems. PMID:27508102

Utilization of non-conventional systems for conversion of biomass to food components: Recovery optimization and characterizations of algal proteins and lipids

NASA Technical Reports Server (NTRS)

Karel, M.; Nakhost, Z.

1986-01-01

Protein isolate obtained from green algae (Scenedesmus obliquus) cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine makes algal protein isolate a high quality component of closed environment life support system (CELSS) diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical CO2 resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Development of high protein, high fiber smoothie as a grab-and-go breakfast option using response surface methodology.

PubMed

Mehta, Dipakkumar; Kumar, M H Sathish; Sabikhi, Latha

2017-11-01

The current work aimed to formulate smoothie by optimizing varying levels of soy protein isolate (1.5-2.5% w/w), sucralose (150-190 ppm) and pectin (0.3-0.5% w/w) along with milk, legume (chickpea), vegetable (carrot), fruit (mango), honey and trisodium citrate by response surface methodology on the basis of sensory (color and appearance, flavor, consistency, sweetness and overall acceptability) and physical (expressible serum and viscosity) responses. Soy protein isolate and pectin levels influenced color and appearance, flavor, consistency and overall acceptability significantly. Soy protein isolate and pectin showed a positive correlation with viscosity of smoothie with reduced expressible serum. Smoothie was optimized with 1.8% (w/w) soy protein isolate, 166.8 ppm sucralose, and 0.5% (w/w) pectin with acceptable quality. One serving (325 ml) of optimized smoothie provides approximately 23% protein, 27% dietary fiber of the recommended daily values and provides approximately 74 kcal per 100 ml of smoothie, which renders smoothie as a high protein, high fiber, grab-and-go breakfast option.

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

DOE PAGES

Reeve, Wayne; Sullivan, John; Ronson, Clive; ...

2015-08-14

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reeve, Wayne; Sullivan, John; Ronson, Clive

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

A multiple functional connector for high-resolution optical satellites

NASA Astrophysics Data System (ADS)

She, Fengke; Zheng, Gangtie

2017-11-01

For earth observation satellites, perturbations from actuators, such as CMGs and momentum wheels, and thermal loadings from support structures often have significant impact on the image quality of an optical. Therefore, vibration isolators and thermal deformation releasing devices nowadays often become important parts of an image satellite. However, all these devices will weak the connection stiffness between the optical instrument and the satellite bus structure. This will cause concern of the attitude control system design for worrying about possible negative effect on the attitude control. Therefore, a connection design satisfying all three requirements is a challenge of advanced image satellites. Chinese scientists have proposed a large aperture high-resolution satellite for earth observation. To meet all these requirements and ensure image quality, specified multiple function connectors are designed to meet these challenging requirements, which are: isolating vibration, releasing thermal deformation and ensuring whole satellite dynamic properties [1]. In this paper, a parallel spring guide flexure is developed for both vibration isolation and thermal deformation releasing. The stiffness of the flexure is designed to meet the vibration isolation requirement. To attenuate vibration, and more importantly to satisfy the stability requirement of the attitude control system, metal damping, which has many merits for space applications, are applied in this connecter to provide a high damping ratio and nonlinear stiffness. The capability of the connecter for vibration isolation and attenuation is validated through numerical simulation and experiments. Connecter parameter optimization is also conducted to meet both requirements of thermal deformation releasing and attitude control. Analysis results show that the in-orbit attitude control requirement is satisfied while the thermal releasing performance is optimized. The design methods and analysis results are also provided in the present paper.

The Impact of Isolation on the Job Satisfaction of New Principals

ERIC Educational Resources Information Center

Bauer, Scott C.; Brazer, S. David

2013-01-01

Professional isolation has hampered the quality of the work experience for employees inside and outside public education for decades. This study explores the role that isolation plays in predicting the quality of the work experience among new principals. The analysis tests whether isolation serves as a mediator in the relationship between factors…

Transcriptional Profiling of Synovial Macrophages Using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis.

PubMed

Mandelin, Arthur M; Homan, Philip J; Shaffer, Alexander M; Cuda, Carla M; Dominguez, Salina T; Bacalao, Emily; Carns, Mary; Hinchcliff, Monique; Lee, Jungwha; Aren, Kathleen; Thakrar, Anjali; Montgomery, Anna B; Bridges, S Louis; Bathon, Joan M; Atkinson, John P; Fox, David A; Matteson, Eric L; Buckley, Christopher D; Pitzalis, Costantino; Parks, Deborah; Hughes, Laura B; Geraldino-Pardilla, Laura; Ike, Robert; Phillips, Kristine; Wright, Kerry; Filer, Andrew; Kelly, Stephen; Ruderman, Eric M; Morgan, Vince; Abdala-Valencia, Hiam; Misharin, Alexander V; Budinger, G Scott; Bartom, Elizabeth T; Pope, Richard M; Perlman, Harris; Winter, Deborah R

2018-06-01

Currently, there are no reliable biomarkers for predicting therapeutic response in patients with rheumatoid arthritis (RA). The synovium may unlock critical information for determining efficacy, since a reduction in the numbers of sublining synovial macrophages remains the most reproducible biomarker. Thus, a clinically actionable method for the collection of synovial tissue, which can be analyzed using high-throughput strategies, must become a reality. This study was undertaken to assess the feasibility of utilizing synovial biopsies as a precision medicine-based approach for patients with RA. Rheumatologists at 6 US academic sites were trained in minimally invasive ultrasound-guided synovial tissue biopsy. Biopsy specimens obtained from patients with RA and synovial tissue from patients with osteoarthritis (OA) were subjected to histologic analysis, fluorescence-activated cell sorting, and RNA sequencing (RNA-seq). An optimized protocol for digesting synovial tissue was developed to generate high-quality RNA-seq libraries from isolated macrophage populations. Associations were determined between macrophage transcriptional profiles and clinical parameters in RA patients. Patients with RA reported minimal adverse effects in response to synovial biopsy. Comparable RNA quality was observed from synovial tissue and isolated macrophages between patients with RA and patients with OA. Whole tissue samples from patients with RA demonstrated a high degree of transcriptional heterogeneity. In contrast, the transcriptional profile of isolated RA synovial macrophages highlighted different subpopulations of patients and identified 6 novel transcriptional modules that were associated with disease activity and therapy. Performance of synovial tissue biopsies by rheumatologists in the US is feasible and generates high-quality samples for research. Through the use of cutting-edge technologies to analyze synovial biopsy specimens in conjunction with corresponding clinical information, a precision medicine-based approach for patients with RA is attainable. © 2018, American College of Rheumatology.

Unity Power Factor Operated PFC Converter Based Power Supply for Computers

NASA Astrophysics Data System (ADS)

Singh, Shikha; Singh, Bhim; Bhuvaneswari, G.; Bist, Vashist

2017-11-01

Power Supplies (PSs) employed in personal computers pollute the single phase ac mains by drawing distorted current at a substandard Power Factor (PF). The harmonic distortion of the supply current in these personal computers are observed 75% to 90% with the Crest Factor (CF) being very high which escalates losses in the distribution system. To find a tangible solution to these issues, a non-isolated PFC converter is employed at the input of isolated converter that is capable of improving the input power quality apart from regulating the dc voltage at its output. This is given to the isolated stage that yields completely isolated and stiffly regulated multiple output voltages which is the prime requirement of computer PS. The operation of the proposed PS is evaluated under various operating conditions and the results show improved performance depicting nearly unity PF and low input current harmonics. The prototype of this PS is developed in laboratory environment and test results are recorded which corroborate the power quality improvement observed in simulation results under various operating conditions.

High-Quality Genome Sequence of the Highly Resistant Bacterium Staphylococcus haemolyticus, Isolated from a Neonatal Bloodstream Infection.

PubMed

Hosseinkhani, Farideh; Emaneini, Mohammad; van Leeuwen, Willem

2017-07-20

Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus , originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence. Copyright © 2017 Hosseinkhani et al.

Queens Tri-School Confederation 1992-93 Evaluation Report. OREA Report.

ERIC Educational Resources Information Center

Dworkowitz, Barbara

This report presents the evaluation results of the Queens Tri-School Confederation magnet programs in New York City: programs designed to reduce minority-group isolation among high school students in three high schools and simultaneously improve the quality of their education through the sharing of resources and expertise. These programs, which…

A highly efficient method for extracting next-generation sequencing quality RNA from adipose tissue of recalcitrant animal species.

PubMed

Sharma, Davinder; Golla, Naresh; Singh, Dheer; Onteru, Suneel K

2018-03-01

The next-generation sequencing (NGS) based RNA sequencing (RNA-Seq) and transcriptome profiling offers an opportunity to unveil complex biological processes. Successful RNA-Seq and transcriptome profiling requires a large amount of high-quality RNA. However, NGS-quality RNA isolation is extremely difficult from recalcitrant adipose tissue (AT) with high lipid content and low cell numbers. Further, the amount and biochemical composition of AT lipid varies depending upon the animal species which can pose different degree of resistance to RNA extraction. Currently available approaches may work effectively in one species but can be almost unproductive in another species. Herein, we report a two step protocol for the extraction of NGS quality RNA from AT across a broad range of animal species. © 2017 Wiley Periodicals, Inc.

High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York

DOE PAGES

Tian, Rui; Parker, Matthew; Seshadri, Rekha; ...

2015-05-16

Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Rui; Parker, Matthew; Seshadri, Rekha

Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

TECHNICAL BRIEF: Isolation of total DNA from postmortem human eye tissues and quality comparison between iris and retina

PubMed Central

Wang, Jay Ching Chieh; Wang, Aikun; Gao, Jiangyuan; Cao, Sijia; Samad, Idris; Zhang, Dean; Ritland, Carol; Cui, Jing Z.

2012-01-01

Background Recent genomic technologies have propelled our understanding of the mechanisms underlying complex eye diseases such as age-related macular degeneration (AMD). Genotyping postmortem eye tissues for known single nucleotide polymorphisms (SNPs) associated with AMD may prove valuable, especially when combined with information obtained through other methods such as immunohistochemistry, western blot, enzyme-linked immunosorbent assay (ELISA), and proteomics. Initially intending to genotype postmortem eye tissues for AMD-related SNPs, our group became interested in isolating and comparing the quality of DNA from the iris and retina of postmortem donor eyes. Since there is no previously published protocol in the literature on this topic, we present a protocol suitable for isolating high-quality DNA from postmortem eye tissues for genomic studies. Methods DNA from 33 retinal samples and 35 iris samples was extracted using the phenol-chloroform-isoamyl method from postmortem donor eye tissues. The quantity of DNA was measured with a spectrophotometer while the quality was checked using gel electrophoresis. The DNA samples were then amplified with PCR for the complement factor H (CFH) gene. The purified amplified products were then genotyped for the SNPs in the CFH gene. Results Regarding concentration, the retina yielded 936 ng/μl of DNA, while the iris yielded 78 ng/μl of DNA. Retinal DNA was also purer than iris DNA (260/280=1.78 vs. 1.46, respectively), and produced superior PCR results. Retinal tissue yielded significantly more DNA than the iris tissue per mg of sample (21.7 ng/μl/mg vs. 7.42 ng/μl/mg). Retinal DNA can be readily amplified with PCR, while iris DNA can also be amplified by adding bovine serum albumin. Overall, retinal tissues yielded DNA of superior quality, quantity, and suitability for genotyping and genomic studies. Conclusions The protocol presented here provides a clear and reliable method for isolating total DNA from postmortem eye tissues. Retinal tissue provides DNA of excellent quantity and quality for genotyping and downstream genomic studies. However, DNA isolated from iris tissues, and treated with bovine serum albumin, may also be a valuable source of DNA for genotyping and genomic studies. PMID:23288996

All-In-One: Advanced preparation of Human Parenchymal and Non-Parenchymal Liver Cells

PubMed Central

Werner, Melanie; Driftmann, Sabrina; Kleinehr, Kathrin; Kaiser, Gernot M.; Mathé, Zotlan; Treckmann, Juergen-Walter; Paul, Andreas; Skibbe, Kathrin; Timm, Joerg; Canbay, Ali; Gerken, Guido; Schlaak, Joerg F.; Broering, Ruth

2015-01-01

Background & Aims Liver cells are key players in innate immunity. Thus, studying primary isolated liver cells is necessary for determining their role in liver physiology and pathophysiology. In particular, the quantity and quality of isolated cells are crucial to their function. Our aim was to isolate a large quantity of high-quality human parenchymal and non-parenchymal cells from a single liver specimen. Methods Hepatocytes, Kupffer cells, liver sinusoidal endothelial cells, and stellate cells were isolated from liver tissues by collagenase perfusion in combination with low-speed centrifugation, density gradient centrifugation, and magnetic-activated cell sorting. The purity and functionality of cultured cell populations were controlled by determining their morphology, discriminative cell marker expression, and functional activity. Results Cell preparation yielded the following cell counts per gram of liver tissue: 2.0±0.4×107 hepatocytes, 1.8±0.5×106 Kupffer cells, 4.3±1.9×105 liver sinusoidal endothelial cells, and 3.2±0.5×105 stellate cells. Hepatocytes were identified by albumin (95.5±1.7%) and exhibited time-dependent activity of cytochrome P450 enzymes. Kupffer cells expressed CD68 (94.5±1.2%) and exhibited phagocytic activity, as determined with 1μm latex beads. Endothelial cells were CD146+ (97.8±1.1%) and exhibited efficient uptake of acetylated low-density lipoprotein. Hepatic stellate cells were identified by the expression of α-smooth muscle actin (97.1±1.5%). These cells further exhibited retinol (vitamin A)-mediated autofluorescence. Conclusions Our isolation procedure for primary parenchymal and non-parenchymal liver cells resulted in cell populations of high purity and quality, with retained physiological functionality in vitro. Thus, this system may provide a valuable tool for determining liver function and disease. PMID:26407160

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.

2015-03-12

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

Enteropathogenic Bacteria Contamination of Unchlorinated Drinking Water in Korea, 2010

PubMed Central

Lee, Si Won; Lee, Do Kyung; An, Hyang Mi; Cha, Min Kyeong; Kim, Kyung Jae

2011-01-01

Objectives The purpose of this study was to assess the microbiological quality of unchlorinated drinking water in Korea, 2010. One hundred and eighty unchlorinated drinking water samples were collected from various sites in Seoul and Gyeonggi province. Methods To investigate bacterial presence, the pour plate method was used with cultures grown on selective media for total bacteria, total coliforms, and Staphylococcus spp., respectively. Results In the 180 total bacteria investigation, 72 samples from Seoul and 33 samples from Gyeonggi province were of an unacceptable quality (>102 CFU/mL). Of all the samples tested, total coliforms were detected in 28 samples (15.6%) and Staphylococcus spp. in 12 samples (6.7%). Most of the coliform isolates exhibited high-level resistance to cefazolin (88.2%), cefonicid (64.7%) and ceftazidime (20.6%). In addition, Staphylococcus spp. isolates exhibited high-level resistance to mupirocin (42%). Species of Pseudomonas, Acinetobacter, Cupriavidus, Hafnia, Rahnella, Serratia, and Yersinia were isolated from the water samples. Conclusions The results of this study suggest that consumption of unchlorinated drinking water could represent a notable risk to the health of consumers. As such, there is need for continuous monitoring of these water sources and to establish standards. PMID:22216417

Expressive electronic journal writing: freedom of communication for survivors of acquired brain injury.

PubMed

Fraas, Michael; Balz, Magdalen A

2008-03-01

In addition to the impaired ability to effectively communicate, adults with acquired brain injury (ABI) also experience high incidences of depression, social isolation, and decreased quality of life. Expressive writing programs have been shown to be effective in alleviating these concomitant impairments in other populations including incarcerated inmates (Lane, Writing as a road to self-discovery, F & W, Cincinnati 1993). In addition, computer applications such as email have been suggested as an effective means of improving communication and social isolation in adults with brain injury (Sohlberg et al. [2003]. Brain Injury, 17(7), 609-629). This investigation examines the effects of on-line expressive journal writing on the communication, emotional status, social integration and quality of life of individuals with brain injury.

Seasonal Variations in Water-Quality, Antibiotic Residues, Resistant Bacteria and Antibiotic Resistance Genes of Escherichia coli Isolates from Water and Sediments of the Kshipra River in Central India.

PubMed

Diwan, Vishal; Hanna, Nada; Purohit, Manju; Chandran, Salesh; Riggi, Emilia; Parashar, Vivek; Tamhankar, Ashok J; Stålsby Lundborg, Cecilia

2018-06-17

To characterize the seasonal variation, over one year, in water-quality, antibiotic residue levels, antibiotic resistance genes and antibiotic resistance in Escherichia coli isolates from water and sediment of the Kshipra River in Central India. Water and sediment samples were collected from seven selected points from the Kshipra River in the Indian city of Ujjain in the summer, rainy season, autumn and winter seasons in 2014. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. High-performance liquid chromatography⁻tandem mass spectrometry was used to determine the concentrations of antibiotic residues. In river water and sediment samples, antibiotic resistance and multidrug resistance patterns of isolated E. coli to 17 antibiotics were tested and genes coding for resistance and phylogenetic groups were detected using multiplex polymerase chain reaction. One-way analysis of variance (ANOVA) and Fisher tests were applied to determine seasonal variation. In river water, seasonal variation was significantly associated with various water quality parameters, presence of sulfamethoxazole residues, bacteria resistant to ampicillin, cefepime, meropenem, amikacin, gentamicin, tigecycline, multidrug resistance and CTX-M-1 gene. The majority of the Extended Spectrum Beta-Lactamase (ESBL)-producing E. coli isolates from river water and sediment in all different seasons belonged to phylogenetic group A or B1. Antibiotic pollution, resistance and resistance genes in the Kshipra River showed significant seasonal variation. Guidelines and regulatory standards are needed to control environmental dissemination of these “pollutants” in this holy river.

Foreskin-isolated keratinocytes provide successful extemporaneous autologous paediatric skin grafts.

PubMed

Mcheik, Jiad N; Barrault, Christine; Pedretti, Nathalie; Garnier, Julien; Juchaux, Franck; Levard, Guillaume; Morel, Franck; Lecron, Jean-Claude; Bernard, François-Xavier

2016-03-01

Severe burns in children are conventionally treated with split-thickness skin autografts or epidermal sheets. However, neither early complete healing nor quality of epithelialization is satisfactory. An alternative approach is to graft isolated keratinocytes. We evaluated paediatric foreskin and auricular skin as donor sources, autologous keratinocyte transplantation, and compared the graft efficiency to the in vitro capacities of isolated keratinocytes to divide and reconstitute epidermal tissue. Keratinocytes were isolated from surgical samples by enzymatic digestion. Living cell recovery, in vitro proliferation and epidermal reconstruction capacities were evaluated. Differentiation status was analysed, using qRT-PCR and immunolabelling. Eleven children were grafted with foreskin-derived (boys) or auricular (girls) keratinocyte suspensions dripped onto deep severe burns. The aesthetic and functional quality of epithelialization was monitored in a standardized way. Foreskin keratinocyte graft in male children provides for the re-epithelialization of partial deep severe burns and accelerates wound healing, thus allowing successful wound closure, and improves the quality of scars. In accordance, in vitro studies have revealed a high yield of living keratinocyte recovery from foreskin and their potential in terms of regeneration and differentiation. We report a successful method for grafting paediatric males presenting large severe burns through direct spreading of autologous foreskin keratinocytes. This alternative method is easy to implement, improves the quality of skin and minimizes associated donor site morbidity. In vitro studies have highlighted the potential of foreskin tissue for graft applications and could help in tissue selection with the prospect of grafting burns for girls. Copyright © 2013 John Wiley & Sons, Ltd.

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

Draft versus finished sequence data for DNA and protein diagnostic signature development

PubMed Central

Gardner, Shea N.; Lam, Marisa W.; Smith, Jason R.; Torres, Clinton L.; Slezak, Tom R.

2005-01-01

Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10−3–10−5 (∼8× coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of ∼1% (3× to 6× coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures. PMID:16243783

Evaluation of Conceptual Frameworks Applicable to the Study of Isolation Precautions Effectiveness

PubMed Central

Crawford, Catherine; Shang, Jingjing

2015-01-01

Aims A discussion of conceptual frameworks applicable to the study of isolation precautions effectiveness according to Fawcett and DeSanto-Madeya’s (2013) evaluation technique and their relative merits and drawbacks for this purpose Background Isolation precautions are recommended to control infectious diseases with high morbidity and mortality, but effectiveness is not established due to numerous methodological challenges. These challenges, such as identifying empirical indicators and refining operational definitions, could be alleviated though use of an appropriate conceptual framework. Design Discussion paper Data Sources In mid-April 2014, the primary author searched five electronic, scientific literature databases for conceptual frameworks applicable to study isolation precautions, without limiting searches by publication date. Implications for Nursing By reviewing promising conceptual frameworks to support isolation precautions effectiveness research, this paper exemplifies the process to choose an appropriate conceptual framework for empirical research. Hence, researchers may build on these analyses to improve study design of empirical research in multiple disciplines, which may lead to improved research and practice. Conclusion Three frameworks were reviewed: the epidemiologic triad of disease, Donabedian’s healthcare quality framework and the Quality Health Outcomes model. Each has been used in nursing research to evaluate health outcomes and contains concepts relevant to nursing domains. Which framework can be most useful likely depends on whether the study question necessitates testing multiple interventions, concerns pathogen-specific characteristics and yields cross-sectional or longitudinal data. The Quality Health Outcomes model may be slightly preferred as it assumes reciprocal relationships, multi-level analysis and is sensitive to cultural inputs. PMID:26179813

Dispersal Limitations on Fish Community Recovery Following Long-term Water Quality Remediation

DOE PAGES

McManamay, Ryan A.; Jett, Robert T.; Ryon, Michael G.; ...

2016-02-22

Holistic restoration approaches, such as water quality remediation, are likely to meet conservation objectives because they are typically implemented at watershed scales, as opposed to individual stream reaches. However, habitat fragmentation may impose constraints on the ecological effectiveness of holistic restoration strategies by limiting colonization following remediation. We questioned the importance of dispersal limitations to fish community recovery following long-term water quality remediation and species reintroductions across the White Oak Creek (WOC) watershed near Oak Ridge, Tennessee (USA). Long-term (26 years) responses in fish species richness and biomass to water quality remediation were evaluated in light of habitat fragmentation andmore » population isolation from instream barriers, which varied in their passage potential. In addition, ordination techniques were used to determine the relative importance of habitat connectivity and water quality, in explaining variation fish communities relative to environmental fluctuations, i.e. streamflow. Ecological recovery (changes in richness) at each site was negatively related to barrier index, a measure of community isolation by barriers relative to stream distance. Following species reintroductions, dispersal by fish species was consistently in the downstream direction and upstream passage above barriers was non-existent. The importance of barrier index in explaining variation in fish communities was stronger during higher flow conditions, but decreased over time an indication of increasing community stability and loss of seasonal migrants. Compared to habitat fragmentation, existing water quality concerns (i.e., outfalls, point source discharges) were unrelated to ecological recovery, but explained relatively high variation in community dynamics. Our results suggest that habitat fragmentation limited the ecological effectiveness of intensive water quality remediation efforts and fish reintroduction efforts by impeding recolonization at isolated stream reaches.« less

Residual risk of bacterial contamination of platelets: six years of experience with sterility testing.

PubMed

Ramirez-Arcos, Sandra; DiFranco, Caesar; McIntyre, Terri; Goldman, Mindy

2017-09-01

Canadian Blood Services screens 100% of platelet concentrates (PCs) for bacterial contamination with the BacT/ALERT system. Quality-control sterility testing of 1% (≥10 units) of outdated PCs is performed monthly. Data from routine screening, quality-control testing, and septic reactions obtained from 2010 to 2016 are presented herein. In total, 601,988 buffy coat PC pools and 186,737 apheresis PCs were routinely screened with aerobic cultures over 6 years. Outdate quality-control testing of 8535 buffy coat and 8498 apheresis PCs was performed using aerobic and anaerobic cultures during the same period. Results were classified as "true-positives" when the same bacterium was isolated in initial and confirmatory cultures or "false-negatives" when bacteria were missed in early screening and were captured during quality-control sterility testing or through investigation of sepsis cases. During routine screening, the true-positive rates between buffy coat (0.94 per 10,000) and apheresis (0.96 per 10,000) PCs were similar (p = 0.9473). Seventy-five bacteria isolated during PC screening included Gram-positive and Gram-negative organisms. Six false-negative septic reactions were reported that implicated coagulase-negative staphylococci (n = 3) and Staphylococcus aureus (n = 3) for approximate rates of 1 per 100,000 transfusion reactions and 1 per 500,000 fatalities. During quality-control testing, the false-negative rates between buffy coat (8 per 10,000) and apheresis (9 per 10,000) PCs were similar (p = 0.7897). All 15 quality-control isolates were Gram-positive bacteria. The current bacterial screening protocol is efficacious for identifying Gram-negative bacteria. However, the high proportion of Gram-positive organisms detected on outdate quality-control testing and septic transfusion events demonstrates a residual safety risk that merits further intervention. © 2017 AABB.

Dispersal Limitations on Fish Community Recovery Following Long-term Water Quality Remediation

DOE Office of Scientific and Technical Information (OSTI.GOV)

McManamay, Ryan A.; Jett, Robert T.; Ryon, Michael G.

Holistic restoration approaches, such as water quality remediation, are likely to meet conservation objectives because they are typically implemented at watershed scales, as opposed to individual stream reaches. However, habitat fragmentation may impose constraints on the ecological effectiveness of holistic restoration strategies by limiting colonization following remediation. We questioned the importance of dispersal limitations to fish community recovery following long-term water quality remediation and species reintroductions across the White Oak Creek (WOC) watershed near Oak Ridge, Tennessee (USA). Long-term (26 years) responses in fish species richness and biomass to water quality remediation were evaluated in light of habitat fragmentation andmore » population isolation from instream barriers, which varied in their passage potential. In addition, ordination techniques were used to determine the relative importance of habitat connectivity and water quality, in explaining variation fish communities relative to environmental fluctuations, i.e. streamflow. Ecological recovery (changes in richness) at each site was negatively related to barrier index, a measure of community isolation by barriers relative to stream distance. Following species reintroductions, dispersal by fish species was consistently in the downstream direction and upstream passage above barriers was non-existent. The importance of barrier index in explaining variation in fish communities was stronger during higher flow conditions, but decreased over time an indication of increasing community stability and loss of seasonal migrants. Compared to habitat fragmentation, existing water quality concerns (i.e., outfalls, point source discharges) were unrelated to ecological recovery, but explained relatively high variation in community dynamics. Our results suggest that habitat fragmentation limited the ecological effectiveness of intensive water quality remediation efforts and fish reintroduction efforts by impeding recolonization at isolated stream reaches.« less

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

PubMed Central

Yu, Nianjun; Zhang, Wei; Xing, Lihua; Xie, Dongmei; Peng, Daiyin

2018-01-01

Acquiring high quality RNA is the basis of plant molecular biology research, plant genetics and other physiological investigations. At present, a large number of nucleotide isolation methods have been exploited or modified, such as commercial kits, CTAB, SDS methods and so on. Due to the nature of different plants, extraction methods vary. Moreover, efficiency of certain approach cannot be guaranteed due to composition of different plants and extracting high quality RNA from plants rich in polysaccharides and polyphenols are often difficult. The physical and chemical properties of polysaccharides which are similar to nucleic acids and other secondary metabolites will be coprecipitated with RNA irreversibly. Therefore, how to remove polysaccharides and other secondary metabolites during RNA extraction is the primary challenge. Dendrobium huoshanense is an Orchidaceae perennial herb that is rich in polysaccharides and other secondary metabolites. By using D. huoshanense as the subject, we improved the method originated from CHAN and made it suitable for plants containing high amount of polysaccharides and polyphenols. The extracted total RNA was clear and non-dispersive, with good integrity and no obvious contamination with DNA and other impurities. And it was also evaluated by gel electrophoresis, nucleic acid quantitative detector and PCR assessment. Thus, as a simple approach, it is suitable and efficient in RNA isolation for plants rich in polysaccharides and polyphenols. PMID:29715304

Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goordial, Jacqueline; Raymond-Bouchard, Isabelle; Riley, Robert

Here, we report the draft genome sequence of Rhodotorula sp. strain JG1b, a yeast that was isolated from ice-cemented permafrost in the upper-elevation McMurdo Dry Valleys, Antarctica. The sequenced genome size is 19.39 Mb, consisting of 156 scaffolds and containing a total of 5,625 predicted genes. This is the first known cold-adapted Rhodotorula sp. sequenced to date.

Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica

DOE PAGES

Goordial, Jacqueline; Raymond-Bouchard, Isabelle; Riley, Robert; ...

2016-03-17

Here, we report the draft genome sequence of Rhodotorula sp. strain JG1b, a yeast that was isolated from ice-cemented permafrost in the upper-elevation McMurdo Dry Valleys, Antarctica. The sequenced genome size is 19.39 Mb, consisting of 156 scaffolds and containing a total of 5,625 predicted genes. This is the first known cold-adapted Rhodotorula sp. sequenced to date.

Production of high quality brain-derived neurotrophic factor (BDNF) and tropomyosin receptor kinase B (TrkB) RNA from isolated populations of rat spinal cord motor neurons obtained by Laser Capture Microdissection (LCM).

PubMed

Mehta, Prachi; Premkumar, Brian; Morris, Renée

2016-08-03

The mammalian central nervous system (CNS) is composed of multiple cellular elements, making it challenging to segregate one particular cell type to study their gene expression profile. For instance, as motor neurons represent only 5-10% of the total cell population of the spinal cord, meaningful transcriptional analysis on these neurons is almost impossible to achieve from homogenized spinal cord tissue. A major challenge faced by scientists is to obtain good quality RNA from small amounts of starting material. In this paper, we used Laser Capture Microdissection (LCM) techniques to identify and isolate spinal cord motor neurons. The present analysis revealed that perfusion with paraformaldehyde (PFA) does not alter RNA quality. RNA integrity numbers (RINs) of tissue samples from rubrospinal tract (RST)-transected, intact spinal cord or from whole spinal cord homogenate were all above 8, which indicates intact, high-quality RNA. Levels of mRNA for brain-derived neurotrophic factor (BDNF) or for its tropomyosin receptor kinase B (TrkB) were not affected by rubrospinal tract (RST) transection, a surgical procedure that deprive motor neurons from one of their main supraspinal input. The isolation of pure populations of neurons with LCM techniques allows for robust transcriptional characterization that cannot be achieved with spinal cord homogenates. Such preparations of pure population of motor neurons will provide valuable tools to advance our understanding of the molecular mechanisms underlying spinal cord injury and neuromuscular diseases. In the near future, LCM techniques might be instrumental to the success of gene therapy for these debilitating conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Hospital hydrotherapy pools treated with ultra violet light: bad bacteriological quality and presence of thermophilic Naegleria.

PubMed Central

De Jonckheere, J. F.

1982-01-01

The microbiological quality of eight halogenated and two u.v.-treated hydrotherapy pools in hospitals was investigated. The microbiological quality of halogenated hydrotherapy pools was comparable to halogenated public swimming pools, although in some Pseudomonas aeruginosa and faecal pollution indicators were more frequent due to bad management. On the other hand u.v.-treated hydrotherapy pools had very bad microbiological quality. Apart from faecal pollution indicators, P. aeruginosa was present in very high numbers. Halogenated hydrotherapy pools were not highly contaminated with amoebae, and Naegleria spp. were never detected. On the other hand u.v.-treated pools contained very high numbers of thermophilic Naegleria. The Naegleria isolated were identified as N. lovaniensis, a species commonly found in association with N. fowleri. Isoenzyme analysis showed a different type of N. lovaniensis was present in each of two u.v.-treated pools. Images Plate 1 PMID:7061835

A feasibility work on the applications of MRE to automotive components

NASA Astrophysics Data System (ADS)

Kim, S. H.; Park, Y. J.; Cha, A. R.; Kim, G. W.; Bang, J. H.; Lim, C. S.; Choi, S. B.

2018-03-01

A feasibility work on the application of magneto-rheological elastomers (MREs) to automotive components, such as engine mounts is presented. While vehicle components require the high resonance frequency in terms of ride quality and handling, it is required to have the low resonance frequency to isolate the incoming vibration. With the conventional automotive technologies, it is challenging to combine these two conflicting performance trade-offs, ride quality including handling, and NVH (noise, vibration and harshness). Over the last decades, MREs, one of the new emerging smart materials, have been widely used to resolve this technical limitation. For example, an advanced engine mount was developed by using MRE to isolate the vibration transmitting from engines. In this paper, we will focus on rear cross member bushes, which is a key component for isolating the vibration from the road, and demonstrate their improved performance by utilizing MRE. The resonance frequency shift induced by the stiffness change of MRE will be presented through the frequency response functions estimated by simulation result.

High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama

DOE PAGES

Tian, Rui; Parker, Matthew; Seshadri, Rekha; ...

2015-05-17

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients.

PubMed

Ssengooba, Willy; de Jong, Bouke C; Joloba, Moses L; Cobelens, Frank G; Meehan, Conor J

2016-08-05

In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments. From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis. Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16-101)/mm(3) and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical. Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly.

Fate of human viruses in groundwater recharge systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaughn, J.M.; Landry, E.F.

1980-03-01

The overall objective of this research program was to determine the ability of a well-managed tertiary effluent-recharge system to return virologically acceptable water to the groundwater aquifer. The study assessed the quality of waters renovated by indigenous recharge operations and investigated a number of virus-soil interrelationships. The elucidation of the interactions led to the establishment of basin operating criteria for optimizing virus removal. Raw influents, chlorinated tertiary effluents, and renovated wastewater from the aquifer directly beneath a uniquely designed recharge test basin were assayed on a weekly basis for the presence of human enteroviruses and coliform bacteria. High concentrations ofmore » viruses were routinely isolated from influents but were isolated only on four occasions from tertiary-treated sewage effluents. In spite of the high quality effluent being recharged, viruses were isolated from the groundwater observation well, indicating their ability to penetrate the unsaturated zone. Results of poliovirus seeding experiments carried out in the test basin clearly indicated the need to operate recharge basins at low (e.g. 1 cm/h) infiltration rates in areas having soil types similar to those found at the study site. The method selected for reducing the test basin infiltration rate involved clogging the basin surface with settled organic material from highly turbid effluent. Alternative methods for slowing infiltration rates are discussed in the text.« less

Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases.

PubMed

Wang, Pan; Qi, Meng; Barboza, Perry; Leigh, Mary Beth; Ungerfeld, Emilio; Selinger, L Brent; McAllister, Tim A; Forster, Robert J

2011-07-01

The rumen is one of the most powerful fibrolytic fermentation systems known. Gene expression analyses, such as reverse transcription PCR (RT-PCR), microarrays, and metatranscriptomics, are techniques that could significantly expand our understanding of this ecosystem. The ability to isolate and stabilize representative RNA samples is critical to obtaining reliable results with these procedures. In this study, we successfully isolated high-quality total RNA from the solid phase of ruminal contents by using an improved RNA extraction method. This method is based on liquid nitrogen grinding of whole ruminal solids without microbial detachment and acid guanidinium - phenol - chloroform extraction combined with column purification. Yields of total RNA were as high as 150 µg per g of fresh ruminal content. The typical large subunit/small subunit rRNA ratio ranged from 1.8 to 2.0 with an RNA integrity number (Agilent Technologies) greater than 8.5. By eliminating the detachment step, the resulting RNA was more representative of the complete ecosystem. Our improved method removed a major barrier limiting analysis of rumen microbial function from a gene expression perspective. The polyA-tailed eukaryotic mRNAs obtained have successfully been applied to next-generation sequencing, and metatranscriptomic analysis of the solid fraction of rumen contents revealed abundant sequences related to rumen fungi.

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

PubMed

Kresse, Stine H; Namløs, Heidi M; Lorenz, Susanne; Berner, Jeanne-Marie; Myklebost, Ola; Bjerkehagen, Bodil; Meza-Zepeda, Leonardo A

2018-01-01

Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.

High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy

DOE PAGES

Yates, Ron; Howieson, John; De Meyer, Sofie E.; ...

2015-07-24

Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genomemore » is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. In conclusion, this rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.« less

Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity.

PubMed

Sahl, Jason W; Johnson, J Kristie; Harris, Anthony D; Phillippy, Adam M; Hsiao, William W; Thom, Kerri A; Rasko, David A

2011-06-04

Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isolates from blood, peri-anal, and wound sources were examined in an attempt to identify genetic features that could be correlated to each isolation source. Pulsed-field gel electrophoresis, multi-locus sequence typing and antibiotic resistance profiles demonstrated genotypic and phenotypic variation. Each isolate was sequenced to high-quality draft status, which allowed for comparative genomic analyses with existing A. baumannii genomes. A high resolution, whole genome alignment method detailed the phylogenetic relationships of sequenced A. baumannii and found no correlation between phylogeny and body site of isolation. This method identified genomic regions unique to both those isolates found on the surface of the skin or in wounds, termed colonization isolates, and those identified from body fluids, termed invasive isolates; these regions may play a role in the pathogenesis and spread of this important pathogen. A PCR-based screen of 74 A. baumanii isolates demonstrated that these unique genes are not exclusive to either phenotype or isolation source; however, a conserved genomic region exclusive to all sequenced A. baumannii was identified and verified. The results of the comparative genome analysis and PCR assay show that A. baumannii is a diverse and genomically variable pathogen that appears to have the potential to cause a range of human disease regardless of the isolation source.

Template-Growth of Highly Ordered Carbon Nanotube Arrays on Silicon POSTPRINT

DTIC Science & Technology

2006-09-01

packed uni- form CNTs that are spatially isolated from each other is to use a growth template. Highly ordered anodic aluminum oxide ( AAO ) template can...process for evaporating thick aluminum of high quality and good adhesion. 15. SUBJECT TERMS Anodic Aluminum Oxide Template, Carbon Nanotubes (CNTs...within the highly ordered nanopores of an alumina oxide template, which is in turn formed on silicon through anodization of aluminum of unprecedented

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isanapong, Jantiya; Goodwin, Lynne A.; Bruce, David

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

PubMed Central

Pereira, Jorge C.; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

2011-01-01

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others. PMID:22174651

High-Pressure-High-Temperature Processing Reduces Maillard Reaction and Viscosity in Whey Protein-Sugar Solutions.

PubMed

Avila Ruiz, Geraldine; Xi, Bingyan; Minor, Marcel; Sala, Guido; van Boekel, Martinus; Fogliano, Vincenzo; Stieger, Markus

2016-09-28

The aim of the study was to determine the influence of pressure in high-pressure-high-temperature (HPHT) processing on Maillard reactions and protein aggregation of whey protein-sugar solutions. Solutions of whey protein isolate containing either glucose or trehalose at pH 6, 7, and 9 were treated by HPHT processing or conventional high-temperature (HT) treatments. Browning was reduced, and early and advanced Maillard reactions were retarded under HPHT processing at all pH values compared to HT treatment. HPHT induced a larger pH drop than HT treatments, especially at pH 9, which was not associated with Maillard reactions. After HPHT processing at pH 7, protein aggregation and viscosity of whey protein isolate-glucose/trehalose solutions remained unchanged. It was concluded that HPHT processing can potentially improve the quality of protein-sugar-containing foods, for which browning and high viscosities are undesired, such as high-protein beverages.

Biochemical and physicochemical analysis of fish protein isolate recovered from red snapper (Lutjanus sp.) by-product using isoelectric solubilization/precipitation method

NASA Astrophysics Data System (ADS)

Pramono, H.; Pujiastuti, D. Y.; Sahidu, A. M.

2018-04-01

The effect of acid- and alkali-process on biochemical and physicochemical characteristics of fish protein isolate from red snapper (Lutjanus sp) by-product was evaluated. Protein recovered by alkali process (16.79%) was higher compared to acid process (13.75%). Reduction of lipid content and total volatile basic nitrogen (TVB-N) exhibited in both treatments indicated both process improved fish protein isolate recovered from red snapper by-product. In addition, the increasing of water holding capacity and oil binding capacity were observed. However, high peroxide value of fish protein isolate was showed in both treatment. This finding indicated that acid and alkali process can be used as a useful method to recover proteins from red snapper by-product. Alkali process gave a protein isolate with better overall quality compared to acid process.

Fast microwave-assisted acidolysis: a new biorefinery approach for the zero-waste utilisation of lignocellulosic biomass to produce high quality lignin and fermentable saccharides.

PubMed

Zhou, Long; Santomauro, Fabio; Fan, Jiajun; Macquarrie, Duncan; Clark, James; Chuck, Christopher J; Budarin, Vitaliy

2017-09-21

Generally, biorefineries convert lignocellulosic biomass into a range of biofuels and further value added chemicals. However, conventional biorefinery processes focus mainly on the cellulose and hemicellulose fractions and therefore produce only low quality lignin, which is commonly burnt to provide process heat. To make full use of the biomass, more attention needs to be focused on novel separation techniques, where high quality lignin can be isolated that is suitable for further valorisation into aromatic chemicals and fuel components. In this paper, three types of lignocellulosic biomass (softwood, hardwood and herbaceous biomass) were processed by microwave-assisted acidolysis to produce high quality lignin. The lignin from the softwood was isolated largely intact in the solid residue after acidolysis. For example, a 10 min microwave-assisted acidolysis treatment produced lignin with a purity of 93% and in a yield of 82%, which is superior to other conventional separation methods reported. Furthermore, py-GC/MS analysis proved that the isolated lignin retained the original structure of native lignin in the feedstock without severe chemical modification. This is a large advantage, and the purified lignin is suitable for further chemical processing. To assess the suitability of this methodology as part of a biorefinery system, the aqueous phase, produced after acidolysis of the softwood, was characterised and assessed for its suitability for fermentation. The broth contained some mono- and di-saccharides but mainly contained organic acids, oligosaccharides and furans. While this is unsuitable for S. cerevisiae and other common ethanol producing yeasts, two oleaginous yeasts with known inhibitor tolerances were selected: Cryptococcus curvatus and Metschnikowia pulcherrima. Both yeasts could grow on the broth, and demonstrated suitable catabolism of the oligosaccharides and inhibitors over 7 days. In addition, both yeasts were shown to be able to produce an oil with a similar composition to that of palm oil. This preliminary work demonstrates new protocols of microwave-assisted acidolysis and therefore offers an effective approach to produce high purity lignin and fermentable chemicals, which is a key step towards developing a zero-waste lignocellulosic biorefinery.

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui

Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. We find the 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

DOE PAGES

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; ...

2015-04-11

Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. We find the 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Comparison of the volatile constituents in cold-pressed bergamot oil and a volatile oil isolated by vacuum distillation.

PubMed

Belsito, Emilia L; Carbone, Concetta; Di Gioia, Maria L; Leggio, Antonella; Liguori, Angelo; Perri, Francesca; Siciliano, Carlo; Viscomi, Maria C

2007-09-19

The vacuum distillation of bergamot peels furnishes a high-quality essential oil that is totally bergapten-free. This oil was compared with that produced by distillation of cold-pressed oils and those commercially available. The oil obtained by vacuum distillation of the bergamot vegetable matrix shows a composition quite similar to that of the cold-pressed oil. It also displays qualitative characteristics that are superior with respect to those normally observed for essential oils isolated by distillation of cold-pressed oils. Oils isolated by the method presented here can constitute ideal candidates in producing foods, for example, Earl Grey tea, and cosmetic preparations.

Demographic consequences of terrestrial habitat loss for pool-breeding amphibians: predicting extinction risks associated with inadequate size of buffer zones.

PubMed

Harper, Elizabeth B; Rittenhouse, Tracy A G; Semlitsch, Raymond D

2008-10-01

Much of the biodiversity associated with isolated wetlands requires aquatic and terrestrial habitat to maintain viable populations. Current federal wetland regulations in the United States do not protect isolated wetlands or extend protection to surrounding terrestrial habitat. Consequently, some land managers, city planners, and policy makers at the state and local levels are making an effort to protect these wetland and neighboring upland habitats. Balancing human land-use and habitat conservation is challenging, and well-informed land-use policy is hindered by a lack of knowledge of the specific risks of varying amounts of habitat loss. Using projections of wood frog (Rana sylvatica) and spotted salamander (Ambystoma maculatum) populations, we related the amount of high-quality terrestrial habitat surrounding isolated wetlands to the decline and risk of extinction of local amphibian populations. These simulations showed that current state-level wetland regulations protecting 30 m or less of surrounding terrestrial habitat are inadequate to support viable populations of pool-breeding amphibians. We also found that species with different life-history strategies responded differently to the loss and degradation of terrestrial habitat. The wood frog, with a short life span and high fecundity, was most sensitive to habitat loss and isolation, whereas the longer-lived spotted salamander with lower fecundity was most sensitive to habitat degradation that lowered adult survival rates. Our model results demonstrate that a high probability of local amphibian population persistence requires sufficient terrestrial habitat, the maintenance of habitat quality, and connectivity among local populations. Our results emphasize the essential role of adequate terrestrial habitat to the maintenance of wetland biodiversity and ecosystem function and offer a means of quantifying the risks associated with terrestrial habitat loss and degradation.

Quality Assurance in the Polio Laboratory. Cell Sensitivity and Cell Authentication Assays.

PubMed

Dunn, Glynis

2016-01-01

The accuracy of poliovirus surveillance is largely dependent on the quality of the cell lines used for virus isolation, which is the foundation of poliovirus diagnostic work. Many cell lines are available for the isolation of enteroviruses, whilst genetically modified L20B cells can be used as a diagnostic tool for the identification of polioviruses. To be confident that cells can consistently isolate the virus of interest, it is necessary to have a quality assurance system in place, which will ensure that the cells in use are not contaminated with other cell lines or microorganisms and that they remain sensitive to the viruses being studied.The sensitivity of cell lines can be assessed by the regular testing of a virus standard of known titer in the cell lines used for virus isolation. The titers obtained are compared to previously obtained titers in the same assay, so that any loss of sensitivity can be detected.However, the detection of cell line cross contamination is more difficult. DNA bar coding is a technique that uses a short DNA sequence from a standardized position in the genome as a molecular diagnostic assay for species-level identification. For almost all groups of higher animals, the cytochrome c oxidase subunit 1 of mitochondrial DNA (CO1) is emerging as the standard barcode region. This region is 648 nucleotide base pairs long in most phylogenetic groups and is flanked by regions of conserved sequences, making it relatively easy to isolate and analyze. DNA barcodes vary among individuals of the same species to a very minor degree (generally less than 1-2 %), and a growing number of studies have shown that the COI sequences of even closely related species differ by several per cent, making it possible to identify different species with high confidence.

The Current Status of Islet Transplantation and its Perspectives

PubMed Central

Kobayashi, Naoya

2008-01-01

Transplantation of human pancreatic isolated islets can restore beta-cell function but it requires chronic immunosuppression. The outcome of islet transplantation mainly depends on both the quality of islet preparations, and the survival of the graft. The quality of islet preparations can be evaluated by the results of isolation, which determines the chance to achieve insulin independence. The survival of islet grafts is reflected by the amount of engrafted functional tissue that maintains metabolic control. Immunosuppressive therapy prevents the immunological rejection of grafts, but impairs their function and impedes their regenerative capacity. Therefore, the selection of high quality islet preparations and the reduction of toxic effects of immunosuppressive regimens might dramatically improve the outcomes. The application of stem cell therapy in islet transplantation may contribute to a better understanding of the mechanisms responsible for tissue homeostasis and immune tolerance. Xenogeneic islets may serve as an unlimited source if immune tolerance can be achieved. This may be a strategy to enable a substantial improvement in function while overcoming potentially deleterious risks. PMID:19099085

Venturia carpophila draft genome sequence

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

Development of an Overall Environmental Quality Index to Examine Health Outcomes

EPA Science Inventory

Background: Environmental exposures tend to cluster and disamenities, such as landfills or industrial plants, are often located in areas with a high percentage of minority and poor residents. While we tend to model isolated environmental factors, no single exposure can be held re...

Derivation and characterization of human embryonic stem cell lines from poor quality embryos.

PubMed

Liu, Weiqiang; Yin, Yifei; Long, Xiaolin; Luo, Yumei; Jiang, Yonghua; Zhang, Wenhong; Du, Hongzi; Li, Shaoying; Zheng, Yuhong; Li, Qing; Chen, Xinjie; Liao, Baoping; Xiao, Guohong; Wang, Weihua; Sun, Xiaofang

2009-04-01

Poor quality embryos discarded from in vitro fertilization (IVF) laboratories are good sources for deriving human embryonic stem cell (hESC) lines. In this study, 166 poor quality embryos donated from IVF centers on day 3 were cultured in a blastocyst medium for 2 days, and 32 early blastocysts were further cultured in a blastocyst optimum culture medium for additional 2 days so that the inner cell masses (ICMs) could be identified and isolated easily. The ICMs of 17 blastocysts were isolated by a mechanical method, while those of the other 15 blastocysts were isolated by immunosurgery. All isolated ICMs were inoculated onto a feeder layer for subcultivation. The rates of ICM attachment, primary ICM colony formation and the efficiency of hESC derivation were similar between the ICMs isolated by the two methods (P>0.05). As a result, four new hESC lines were established. Three cell lines had normal karyotypes and one had an unbalanced Robertsonian translocation. All cell lines showed normal hESC characteristics and had the differentiation ability. In conclusion, we established a stable and effective method for hESC isolation and culture, and it was confirmed that the mechanical isolation was an effective method to isolate ICMs from poor embryos. These results further indicate that hESC lines can be derived from poor quality embryos discarded by IVF laboratories.

Diversity and Antimicrobial Activities of Actinobacteria Isolated from Tropical Mangrove Sediments in Malaysia

PubMed Central

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135T that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites. PMID:25162061

Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia.

PubMed

Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Eng, Shu-Kee; Goh, Bey-Hing; Yin, Wai-Fong; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan

2014-01-01

The aim of this study was to isolate and identify Actinobacteria from Malaysia mangrove forest and screen them for production of antimicrobial secondary metabolites. Eighty-seven isolates were isolated from soil samples collected at 4 different sites. This is the first report to describe the isolation of Streptomyces, Mycobacterium, Leifsonia, Microbacterium, Sinomonas, Nocardia, Terrabacter, Streptacidiphilus, Micromonospora, Gordonia, and Nocardioides from mangrove in east coast of Malaysia. Of 87 isolates, at least 5 isolates are considered as putative novel taxa. Nine Streptomyces sp. isolates were producing potent antimicrobial secondary metabolites, indicating that Streptomyces isolates are providing high quality metabolites for drug discovery purposes. The discovery of a novel species, Streptomyces pluripotens sp. nov. MUSC 135(T) that produced potent secondary metabolites inhibiting the growth of MRSA, had provided promising metabolites for drug discovery research. The biosynthetic potential of 87 isolates was investigated by the detection of polyketide synthetase (PKS) and nonribosomal polyketide synthetase (NRPS) genes, the hallmarks of secondary metabolites production. Results showed that many isolates were positive for PKS-I (19.5%), PKS-II (42.5%), and NRPS (5.7%) genes, indicating that mangrove Actinobacteria have significant biosynthetic potential. Our results highlighted that mangrove environment represented a rich reservoir for isolation of Actinobacteria, which are potential sources for discovery of antimicrobial secondary metabolites.

MICROBIOLOGICAL ASSESSMENT OF LETTUCE SALADS AND ANTIMICROBIAL RESISTANCE OF STAPHYLOCOCCUS SPP.

PubMed

Guimarães César, Josi; Madruga Peres, Andriele; Pereira das Neves, Caroline; Tupiniquim Freitas de Abreu, Érica; Fagundes de Mello, Jozi; Nunes Moreira, Ângela; Lameiro Rodrigues, Kelly

2015-11-01

self-service restaurants in which food is served ready to be consumed are liable to have some products contaminated by pathogenic microorganisms causing food-transmitted diseases. evaluates the microbiological quality of lettuce salads in restaurants in Pelotas RS Brazil by counts of thermo-tolerant coliforms, E. coli, Staphylococcus spp. and detection of Salmonella spp. Antimicrobial resistance of Staphylococcus spp. isolates are also assessed. thirty-six samples of lettuce salads were collected from nine restaurants and thermotolerant coliforms, Escherichia coli and Staphylococcus spp. were quantified, coupled to a research on Salmonella spp., following methodology by the Bacteriological Analytical Manual. Staphylococcus spp. isolates underwent antimicrobial resistance test by the disc-diffusion method. results showed that 61.1% of the salad samples contained more thermotolerant coliforms than allowed by Brazilian legislation and E. coli was confirmed in 5.6% of the samples. Positive and negative coagulase Staphylococcus occurred respectively in 5.6% and 77.8% of isolates, but no sample had Salmonella spp. Further, 56.7% of the thirty isolates of Staphylococcus spp. tested were resistant to penicillin; 46.7% to oxacillin; 26.7% to erythromycin and 23.3% were multi- resistant. inadequate quality of the salad was due to pathogenic microorganisms, while Staphylococcus spp. isolates had a high percentage of antimicrobial resistance. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells

PubMed Central

2010-01-01

Background In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry. To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process. To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. Results In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared. During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation. During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity. High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. Conclusions The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells. PMID:20831775

Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells.

PubMed

Peternel, Spela; Komel, Radovan

2010-09-10

In recent years bacterial inclusion bodies (IBs) were recognised as highly pure deposits of active proteins inside bacterial cells. Such active nanoparticles are very interesting for further downstream protein isolation, as well as for many other applications in nanomedicine, cosmetic, chemical and pharmaceutical industry.To prepare large quantities of a high quality product, the whole bioprocess has to be optimised. This includes not only the cultivation of the bacterial culture, but also the isolation step itself, which can be of critical importance for the production process.To determine the most appropriate method for the isolation of biologically active nanoparticles, three methods for bacterial cell disruption were analyzed. In this study, enzymatic lysis and two mechanical methods, high-pressure homogenization and sonication, were compared.During enzymatic lysis the enzyme lysozyme was found to attach to the surface of IBs, and it could not be removed by simple washing. As this represents an additional impurity in the engineered nanoparticles, we concluded that enzymatic lysis is not the most suitable method for IBs isolation.During sonication proteins are released (lost) from the surface of IBs and thus the surface of IBs appears more porous when compared to the other two methods. We also found that the acoustic output power needed to isolate the IBs from bacterial cells actually damages proteins structures, thereby causing a reduction in biological activity.High-pressure homogenization also caused some damage to IBs, however the protein loss from the IBs was negligible. Furthermore, homogenization had no side-effects on protein biological activity. The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells.

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

PubMed

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability.

PubMed

Aslan, O; Hamill, R M; Sweeney, T; Reardon, W; Mullen, A M

2009-01-01

It is essential to isolate high-quality DNA from muscle tissue for PCR-based applications in traceability of animal origin. We wished to examine the impact of cooking meat to a range of core temperatures on the quality and quantity of subsequently isolated genomic (specifically, nuclear) DNA. Triplicate steak samples were cooked in a water bath (100 degrees C) until their final internal temperature was 75, 80, 85, 90, 95, or 100 degrees C, and DNA was extracted. Deoxyribonucleic acid quantity was significantly reduced in cooked meat samples compared with raw (6.5 vs. 56.6 ng/microL; P < 0.001), but there was no relationship with cooking temperature. Quality (A(260)/A(280), i.e., absorbance at 260 and 280 nm) was also affected by cooking (P < 0.001). For all 3 genes, large PCR amplicons (product size >800 bp) were observed only when using DNA from raw meat and steak cooked to lower core temperatures. Small amplicons (<200 bp) were present for all core temperatures. Cooking meat to high temperatures thus resulted in a reduced overall yield and probable fragmentation of DNA to sizes less than 800 bp. Although nuclear DNA is preferable to mitochondrial DNA for food authentication, it is less abundant, and results suggest that analyses should be designed to use small amplicon sizes for meat cooked to high core temperatures.

High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

PubMed Central

Castro, Daniel B.A.; Pereira, Letícia Bianca; Silva, Marcus Vinícius M. e; Silva, Bárbara P. da; Palermo, Bruna Rafaella Z.; Carlos, Camila; Belgini, Daiane R.B.; Limache, Elmer Erasmo G.; Lacerda, Gileno V. Jr; Nery, Mariana B.P.; Gomes, Milene B.; Souza, Salatiel S. de; Silva, Thiago M. da; Rodrigues, Viviane D.; Paulino, Luciana C.; Vicentini, Renato; Ferraz, Lúcio F.C.; Ottoboni, Laura M.M.

2015-01-01

An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest. PMID:26484219

METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES

PubMed Central

Li, Yu; Kowdley, Kris V.

2012-01-01

MicroRNAs are a group of intracellular non-coding RNA molecules that have been implicated in a variety of human diseases. Due to their high stability in blood, microRNAs released into circulation could be potentially utilized as non-invasive biomarkers for diagnosis or prognosis. Current microRNA isolation protocols are specifically designed for solid tissues and are impractical for biomarker development utilizing small-volume serum samples on a large scale. Thus, a protocol for microRNA isolation from serum is needed to accommodate these conditions in biomarker development. To establish such a protocol, we developed a simplified approach to normalize sample input by using single synthetic spike-in microRNA. We evaluated three commonly used commercial microRNA isolation kits for the best performance by comparing RNA quality and yield. The manufacturer’s protocol was further modified to improve the microRNA yield from 200 μL of human serum. MicroRNAs isolated from a large set of clinical serum samples were tested on the miRCURY LNA real-time PCR panel and confirmed to be suitable for high-throughput microRNA profiling. In conclusion, we have established a proven method for microRNA isolation from clinical serum samples suitable for microRNA biomarker development. PMID:22982505

Influenza virus isolation.

PubMed

Krauss, Scott; Walker, David; Webster, Robert G

2012-01-01

The isolation of influenza viruses is important for the diagnosis of respiratory diseases in lower animals and humans, for the detection of the infecting agent in surveillance programs, and is an essential element in the development and production of vaccine. Since influenza is caused by a zoonotic virus it is necessary to do surveillance in the reservoir species (aquatic waterfowls), intermediate hosts (quails, pigs), and in affected mammals including humans. Two of the hemagglutinin (HA) subtypes of influenza A viruses (H5 and H7) can evolve into highly pathogenic (HP) strains for gallinaceous poultry; some HP H5 and H7 strains cause lethal infection of humans. In waterfowls, low pathogenic avian influenza (LPAI) isolates are obtained primarily from the cloaca (or feces); in domestic poultry, the virus is more often recovered from the respiratory tract than from cloacal samples; in mammals, the virus is most often isolated from the respiratory tract, and in cases of high pathogenic avian influenza (HPAI) from the blood and internal organs of infected birds. Virus isolation procedures are performed by inoculation of clinical specimens into embryonated eggs (primarily chicken eggs) or onto a variety of primary or continuous tissue culture systems. Successful isolation of influenza virus depends on the quality of the sample and matching the appropriate culture method to the sample type.

Two New Nuclear Isolation Buffers for Plant DNA Flow Cytometry: A Test with 37 Species

PubMed Central

Loureiro, João; Rodriguez, Eleazar; Doležel, Jaroslav; Santos, Conceição

2007-01-01

Background and Aims After the initial boom in the application of flow cytometry in plant sciences in the late 1980s and early 1990s, which was accompanied by development of many nuclear isolation buffers, only a few efforts were made to develop new buffer formulas. In this work, recent data on the performance of nuclear isolation buffers are utilized in order to develop new buffers, general purpose buffer (GPB) and woody plant buffer (WPB), for plant DNA flow cytometry. Methods GPB and WPB were used to prepare samples for flow cytometric analysis of nuclear DNA content in a set of 37 plant species that included herbaceous and woody taxa with leaf tissues differing in structure and chemical composition. The following parameters of isolated nuclei were assessed: forward and side light scatter, propidium iodide fluorescence, coefficient of variation of DNA peaks, quantity of debris background, and the number of particles released from sample tissue. The nuclear genome size of 30 selected species was also estimated using the buffer that performed better for a given species. Key Results In unproblematic species, the use of both buffers resulted in high quality samples. The analysis of samples obtained with GPB usually resulted in histograms of DNA content with higher or similar resolution than those prepared with the WPB. In more recalcitrant tissues, such as those from woody plants, WPB performed better and GPB failed to provide acceptable results in some cases. Improved resolution of DNA content histograms in comparison with previously published buffers was achieved in most of the species analysed. Conclusions WPB is a reliable buffer which is also suitable for the analysis of problematic tissues/species. Although GPB failed with some plant species, it provided high-quality DNA histograms in species from which nuclear suspensions are easy to prepare. The results indicate that even with a broad range of species, either GPB or WPB is suitable for preparation of high-quality suspensions of intact nuclei suitable for DNA flow cytometry. PMID:17684025

Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits

PubMed Central

Bulgari, Daniela; Minio, Andrea; Casati, Paola; Quaglino, Fabio; Delledonne, Massimo

2014-01-01

Endophytic bacteria are microorganisms residing in plant tissues without causing disease symptoms. Here, we provide the high-quality genome sequence of Curtobacterium sp. strain S6, isolated from grapevine plant. The genome assembly contains 2,759,404 bp in 13 contigs and 2,456 predicted genes. PMID:25035321

Genomic Diversity of Biocontrol Strains of Pseudomonas spp. Isolated from Aerial or Root Surfaces of Plants

USDA-ARS?s Scientific Manuscript database

The striking ecological, metabolic, and biochemical diversity of Pseudomonas has intrigued microbiologists for many decades. To explore the genomic diversity of biocontrol strains of Pseudomonas spp., we derived high quality draft sequences of seven strains known to suppress plant disease. The str...

Photography To Enhance Aesthetic Skills.

ERIC Educational Resources Information Center

McIsaac, Marina Stock

Recognizing that photography in the classroom is highly motivating in that it offers a unique vehicle for communicating ideas visually, this study was designed to isolate variables which can be both observed and evaluated in photographs and for which instruction can be designed. Relationships among the technical and aesthetic qualities in…

Literacy by Design: A Universal Design for Learning Approach for Students with Significant Intellectual Disabilities

ERIC Educational Resources Information Center

Coyne, Peggy; Pisha, Bart; Dalton, Bridget; Zeph, Lucille A.; Smith, Nancy Cook

2012-01-01

Literacy instruction for students with significant intellectual disabilities traditionally emphasizes isolated skills instruction focusing on sight words and basic vocabulary. Recent research suggests these students benefit from high-quality instruction that includes comprehension and storybook reading. This study examined the effect of a…

Resource quality or competition: why increase resource acceptance in the presence of conspecifics?

PubMed Central

Nufio, César R.; Papaj, Daniel R.

2011-01-01

Some animal species increase resource acceptance rates in the presence of conspecifics. Such responses may be adaptive if the presence of conspecifics is a reliable indicator of resource quality. Similarly, these responses could represent an adaptive reduction in choosiness under high levels of scramble competition. Although high resource quality and high levels of scramble competition should both favor increased resource acceptance, the contexts in which the increase occurs should differ. In this paper, we tested the effect of social environment on egg-laying and aggressive behavior in the walnut fly, Rhagoletis juglandis, in multiple contexts to determine whether increased resource acceptance in the presence of conspecifics was better viewed as a response to increased host quality or increased competition. We found that grouped females oviposit more readily than isolated females when provided small (low-quality) artificial hosts but not when provided large (high-quality) artificial hosts, indicating that conspecific presence reduces choosiness. Increased resource acceptance was observed even when exposure to conspecifics was temporally or spatially separate from exposure to the resource. Finally, we found that individuals showed reduced aggression after being housed in groups, as expected under high levels of scramble competition. These results indicate that the pattern of resource acceptance in the presence of conspecifics may be better viewed as a response to increased scramble competition rather than as a response to public information about resource quality. PMID:22479135

Resource quality or competition: why increase resource acceptance in the presence of conspecifics?

PubMed

Davis, Jeremy M; Nufio, César R; Papaj, Daniel R

2011-07-01

Some animal species increase resource acceptance rates in the presence of conspecifics. Such responses may be adaptive if the presence of conspecifics is a reliable indicator of resource quality. Similarly, these responses could represent an adaptive reduction in choosiness under high levels of scramble competition. Although high resource quality and high levels of scramble competition should both favor increased resource acceptance, the contexts in which the increase occurs should differ. In this paper, we tested the effect of social environment on egg-laying and aggressive behavior in the walnut fly, Rhagoletis juglandis, in multiple contexts to determine whether increased resource acceptance in the presence of conspecifics was better viewed as a response to increased host quality or increased competition. We found that grouped females oviposit more readily than isolated females when provided small (low-quality) artificial hosts but not when provided large (high-quality) artificial hosts, indicating that conspecific presence reduces choosiness. Increased resource acceptance was observed even when exposure to conspecifics was temporally or spatially separate from exposure to the resource. Finally, we found that individuals showed reduced aggression after being housed in groups, as expected under high levels of scramble competition. These results indicate that the pattern of resource acceptance in the presence of conspecifics may be better viewed as a response to increased scramble competition rather than as a response to public information about resource quality.

A Future Large-Aperture UVOIR Space Observatory: Key Technologies and Capabilities

NASA Technical Reports Server (NTRS)

Bolcar, Matthew Ryan; Stahle, Carl M.; Balasubramaniam, Kunjithapatham; Clampin, Mark; Feinberg, Lee D.; Mosier, Gary E.; Quijada, Manuel A.; Rauscher, Bernard J.; Redding, David C.; Rioux, Norman M.;

The Advanced Technology Large-Aperture Space Telescope (ATLAST) Technology Roadmap

NASA Technical Reports Server (NTRS)

Stahle, Carl; Balasubramanian, K.; Bolcar, M.; Clampin, M.; Feinberg, L.; Hartman, K.; Mosier, C.; Quijada, M.; Rauscher, B.; Redding, D.;

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Rui; Parker, Matthew; Seshadri, Rekha

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nouioui, Imen; Göker, Markus; Carro, Lorena

Nakamurella lactea DLS-10 T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10 T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10 T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

DOE PAGES

Nouioui, Imen; Göker, Markus; Carro, Lorena; ...

2017-01-06

Nakamurella lactea DLS-10 T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10 T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10 T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

The DNA isolation method has effect on allele drop-out and on the results of fluorescent PCR and DNA fragment analysis.

PubMed

Nagy, Bálint; Bán, Zoltán; Papp, Zoltán

2005-10-01

The quality and the quantity of isolated DNA have an effect on PCR amplifications. The authors studied three DNA isolation protocols (resin binding method using fresh and frozen amniotic fluid samples, and silica adsorption method using fresh samples) on the quantity and on the quality of the isolated DNA. Amniotic fluid samples were obtained from 20 pregnant women. The isolated DNA concentrations were determined by real-time fluorimeter using SYBRGreen I method. Each sample was studied for the presence of 8 STR markers. The authors compared the number of the detected alleles, electrophoretograms and peak areas. There was a significant difference between the concentration of the obtained DNA and in the peak areas between the three isolation protocols. The numbers of detected alleles were different, we observed the most allele drop outs in the resin type DNA isolation protocol from the fresh sample (detected allele numbers 182), followed by resin binding protocol from the frozen samples (detected allele number 243) and by the silica adsorption method (detected allele number 264). The authors demonstrated that the DNA isolation method has an effect on the quantity and quality of the isolated DNA, and on further PCR amplifications.

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE PAGES

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; ...

2015-06-04

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform.

PubMed

Rutvisuttinunt, Wiriya; Chinnawirotpisan, Piyawan; Simasathien, Sriluck; Shrestha, Sanjaya K; Yoon, In-Kyu; Klungthong, Chonticha; Fernandez, Stefan

2013-11-01

Active global surveillance and characterization of influenza viruses are essential for better preparation against possible pandemic events. Obtaining comprehensive information about the influenza genome can improve our understanding of the evolution of influenza viruses and emergence of new strains, and improve the accuracy when designing preventive vaccines. This study investigated the use of deep sequencing by the next-generation sequencing (NGS) Illumina MiSeq Platform to obtain complete genome sequence information from influenza virus isolates. The influenza virus isolates were cultured from 6 respiratory acute clinical specimens collected in Thailand and Nepal. DNA libraries obtained from each viral isolate were mixed and all were sequenced simultaneously. Total information of 2.6 Gbases was obtained from a 455±14 K/mm2 density with 95.76% (8,571,655/8,950,724 clusters) of the clusters passing quality control (QC) filters. Approximately 93.7% of all sequences from Read1 and 83.5% from Read2 contained high quality sequences that were ≥Q30, a base calling QC score standard. Alignments analysis identified three seasonal influenza A H3N2 strains, one 2009 pandemic influenza A H1N1 strain and two influenza B strains. The nearly entire genomes of all six virus isolates yielded equal or greater than 600-fold sequence coverage depth. MiSeq Platform identified seasonal influenza A H3N2, 2009 pandemic influenza A H1N1and influenza B in the DNA library mixtures efficiently. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Designer nanoparticle: nanobiotechnology tool for cell biology

NASA Astrophysics Data System (ADS)

Thimiri Govinda Raj, Deepak B.; Khan, Niamat Ali

2016-09-01

This article discusses the use of nanotechnology for subcellular compartment isolation and its application towards subcellular omics. This technology review significantly contributes to our understanding on use of nanotechnology for subcellular systems biology. Here we elaborate nanobiotechnology approach of using superparamagnetic nanoparticles (SPMNPs) optimized with different surface coatings for subcellular organelle isolation. Using pulse-chase approach, we review that SPMNPs interacted differently with the cell depending on its surface functionalization. The article focuses on the use of functionalized-SPMNPs as a nanobiotechnology tool to isolate high quality (both purity and yield) plasma membranes and endosomes or lysosomes. Such nanobiotechnology tool can be applied in generating subcellular compartment inventories. As a future perspective, this strategy could be applied in areas such as immunology, cancer and stem cell research.

All-in-One Nanowire-Decorated Multifunctional Membrane for Rapid Cell Lysis and Direct DNA Isolation

PubMed Central

2015-01-01

This paper describes a handheld device that uses an all-in-one membrane for continuous mechanical cell lysis and rapid DNA isolation without the assistance of power sources, lysis reagents, and routine centrifugation. This nanowire-decorated multifunctional membrane was fabricated to isolate DNA by selective adsorption to silica surface immediately after disruption of nucleus membranes by ultrasharp tips of nanowires for a rapid cell lysis, and it can be directly assembled with commercial syringe filter holders. The membrane was fabricated by photoelectrochemical etching to create microchannel arrays followed by hydrothermal synthesis of nanowires and deposition of silica. The proposed membrane successfully purifies high-quality DNA within 5 min, whereas a commercial purification kit needs more than an hour. PMID:25420232

Designer nanoparticle: nanobiotechnology tool for cell biology.

PubMed

Thimiri Govinda Raj, Deepak B; Khan, Niamat Ali

2016-01-01

This article discusses the use of nanotechnology for subcellular compartment isolation and its application towards subcellular omics. This technology review significantly contributes to our understanding on use of nanotechnology for subcellular systems biology. Here we elaborate nanobiotechnology approach of using superparamagnetic nanoparticles (SPMNPs) optimized with different surface coatings for subcellular organelle isolation. Using pulse-chase approach, we review that SPMNPs interacted differently with the cell depending on its surface functionalization. The article focuses on the use of functionalized-SPMNPs as a nanobiotechnology tool to isolate high quality (both purity and yield) plasma membranes and endosomes or lysosomes. Such nanobiotechnology tool can be applied in generating subcellular compartment inventories. As a future perspective, this strategy could be applied in areas such as immunology, cancer and stem cell research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

S. K. Kushwaha; Pletikosic, I.; Liang, T.

A long-standing issue in topological insulator research has been to find a bulk single crystal material that provides a high quality platform for characterizing topological surface states without interference from bulk electronic states. This material would ideally be a bulk insulator, have a surface state Dirac point energy well isolated from the bulk valence and conduction bands, display quantum oscillations from the surface state electrons, and be growable as large, high quality bulk single crystals. Here we show that this materials obstacle is overcome by bulk crystals of lightly Sn-doped Bi 1.1Sb 0.9Te 2S grown by the Vertical Bridgeman method.more » We characterize Sn-BSTS via angle-resolved photoemission spectroscopy, scanning tunneling microscopy, transport studies, X-ray diffraction, and Raman scattering. We present this material as a high quality topological insulator that can be reliably grown as bulk single crystals and thus studied by many researchers interested in topological surface states.« less

Microbiological quality of indoor air in university libraries.

PubMed

Hayleeyesus, Samuel Fekadu; Manaye, Abayneh Melaku

2014-05-01

To evaluate the concentration of bacteria and fungi in the indoor environment of Jimma University libraries, so as to estimate the health hazard and to create standards for indoor air quality control. The microbial quality of indoor air of eight libraries of Jimma University was determined. The settle plate method using open Petri-dishes containing different culture media was employed to collect sample twice daily. Isolates were identified according to standard methods. The concentrations of bacteria and fungi aerosols in the indoor environment of the university libraries ranged between 367-2595 CFU/m(3). According to the sanitary standards classification of European Commission, almost all the libraries indoor air of Jimma University was heavily contaminated with bacteria and fungi. In spite of their major source difference, the average fungi density found in the indoor air of libraries did appear to follow the same trend with bacterial density (P=0.001). The bacteria isolates included Micrococcus sp., Staphylococcus aureus, Streptococcus pyogenes, Bacillus sp. and Neisseria sp. while Cladosporium sp., Alternaria sp., Penicillium sp. and Aspergillus sp. were the most isolated fungi. The indoor air of all libraries were in the range above highly contaminated according to European Commission classification and the most isolates are considered as potential candidates involved in the establishment of sick building syndromes and often associated with clinical manifestations like allergy, rhinitis, asthma and conjunctivitis. Thus, attention must be given to control those environmental factors which favor the growth and multiplication of microbes in indoor environment of libraries to safeguard the health of users and workers.

Seabirds fighting for land: phenotypic consequences of breeding area constraints at a small remote archipelago.

PubMed

Nunes, Guilherme Tavares; Bertrand, Sophie; Bugoni, Leandro

2018-01-12

Identifying associations between phenotypes and environmental parameters is crucial for understanding how natural selection acts at the individual level. In this context, genetically isolated populations can be useful models for identifying the forces selecting fitness-related traits. Here, we use a comprehensive dataset on a genetically and ecologically isolated population of the strictly marine bird, the brown booby Sula leucogaster, at the tropical and remote Saint Peter and Saint Paul Archipelago, mid-Atlantic Ocean, in order to detect phenotypic adjustments from interindividual differences in diet, foraging behaviour, and nest quality. For this, we took biometrics of all individuals of the colony breeding in 2014 and 2015 and tested their associations with nest quality, diet parameters, and foraging behaviour. While body size was not related to the foraging parameters, the body size of the females (responsible for nest acquisition and defence) was significantly associated with the nest quality, as larger females occupied high-quality nests. Our findings suggest that the small breeding area, rather than prey availability, is a limiting factor, emphasizing the role of on-land features in shaping phenotypic characteristics and fitness in land-dependent marine vertebrates.

Laser Processing of Multilayered Thermal Spray Coatings: Optimal Processing Parameters

NASA Astrophysics Data System (ADS)

Tewolde, Mahder; Zhang, Tao; Lee, Hwasoo; Sampath, Sanjay; Hwang, David; Longtin, Jon

2017-12-01

Laser processing offers an innovative approach for the fabrication and transformation of a wide range of materials. As a rapid, non-contact, and precision material removal technology, lasers are natural tools to process thermal spray coatings. Recently, a thermoelectric generator (TEG) was fabricated using thermal spray and laser processing. The TEG device represents a multilayer, multimaterial functional thermal spray structure, with laser processing serving an essential role in its fabrication. Several unique challenges are presented when processing such multilayer coatings, and the focus of this work is on the selection of laser processing parameters for optimal feature quality and device performance. A parametric study is carried out using three short-pulse lasers, where laser power, repetition rate and processing speed are varied to determine the laser parameters that result in high-quality features. The resulting laser patterns are characterized using optical and scanning electron microscopy, energy-dispersive x-ray spectroscopy, and electrical isolation tests between patterned regions. The underlying laser interaction and material removal mechanisms that affect the feature quality are discussed. Feature quality was found to improve both by using a multiscanning approach and an optional assist gas of air or nitrogen. Electrically isolated regions were also patterned in a cylindrical test specimen.

Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes.

PubMed

Valero-Jiménez, Claudio A; Faino, Luigi; Spring In't Veld, Daphne; Smit, Sandra; Zwaan, Bas J; van Kan, Jan A L

2016-12-01

Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence. A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented. Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.

Isolation and characterization of EMS-induced Dy10 and Ax1 high molecular weight glutenin subunit deficient mutant lines of elite hexaploid wheat (Triticum aestivum L.) cv. Summit

USDA-ARS?s Scientific Manuscript database

The mixing properties of the dough are critical in the production of bread and other food products derived from wheat. The high molecular weight glutenin subunits (HMW-GS) are major determinants of wheat dough processing qualities. The different alleles of the HMW-GS genes in hexaploid wheat vary ...

Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574

PubMed Central

Chiu, Shih-Hau; Wang, Li-Ting; Huang, Lina

2017-01-01

ABSTRACT Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences of L. salivarius BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate. PMID:29167259

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

PubMed Central

Esplin, Ian N. D.; Berg, Jordan A.; Sharma, Ruchira; Allen, Robert C.; Arens, Daniel K.; Ashcroft, Cody R.; Bairett, Shannon R.; Beatty, Nolan J.; Bickmore, Madeline; Bloomfield, Travis J.; Brady, T. Scott; Bybee, Rachel N.; Carter, John L.; Choi, Minsey C.; Duncan, Steven; Fajardo, Christopher P.; Foy, Brayden B.; Fuhriman, David A.; Gibby, Paul D.; Grossarth, Savannah E.; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A.; Hurst, Emily; Hyde, Jonathan R.; Ingersoll, Kayleigh; Jacobson, Caitlin M.; James, Brady D.; Jarvis, Todd M.; Jaen-Anieves, Daniella; Jensen, Garrett L.; Knabe, Bradley K.; Kruger, Jared L.; Merrill, Bryan D.; Pape, Jenny A.; Payne Anderson, Ashley M.; Payne, David E.; Peck, Malia D.; Pollock, Samuel V.; Putnam, Micah J.; Ransom, Ethan K.; Ririe, Devin B.; Robinson, David M.; Rogers, Spencer L.; Russell, Kerri A.; Schoenhals, Jonathan E.; Shurtleff, Christopher A.; Simister, Austin R.; Smith, Hunter G.; Stephenson, Michael B.; Staley, Lyndsay A.; Stettler, Jason M.; Stratton, Mallorie L.; Tateoka, Olivia B.; Tatlow, P. J.; Taylor, Alexander S.; Thompson, Suzanne E.; Townsend, Michelle H.; Thurgood, Trever L.; Usher, Brittian K.; Whitley, Kiara V.; Ward, Andrew T.; Ward, Megan E. H.; Webb, Charles J.; Wienclaw, Trevor M.; Williamson, Taryn L.; Wells, Michael J.; Wright, Cole K.; Breakwell, Donald P.; Hope, Sandra

2017-01-01

ABSTRACT Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. PMID:29146842

Curtobacterium sp. Genome Sequencing Underlines Plant Growth Promotion-Related Traits.

PubMed

Bulgari, Daniela; Minio, Andrea; Casati, Paola; Quaglino, Fabio; Delledonne, Massimo; Bianco, Piero A

2014-07-17

Endophytic bacteria are microorganisms residing in plant tissues without causing disease symptoms. Here, we provide the high-quality genome sequence of Curtobacterium sp. strain S6, isolated from grapevine plant. The genome assembly contains 2,759,404 bp in 13 contigs and 2,456 predicted genes. Copyright © 2014 Bulgari et al.

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

KrF laser amplifier with phase-conjugate Brillouin retroreflectors.

PubMed

Gower, M C

1982-09-01

We have demonstrated the use of phase-conjugate stimulated Brillouin scattering mirrors to produce high-quality, short-pulse KrF laser beams from angular multiplexed and regenerative amplifiers. The mirror was also shown to isolate systems optically from amplifier spontaneous emission. Automatic alignment of targets using this mirror as a retroreflector was also demonstrated.

Use of nested PCR to detect Ceratocystis fagacearum in sapwood of diseased northern oak species

USDA-ARS?s Scientific Manuscript database

Early and accurate diagnosis of oak wilt, caused by Ceratocystis fagacearum (Cf), is important when disease control action is planned. When laboratory diagnosis is needed, standard isolation protocols that are used rely on high quality samples and require > 14 days for incubation. Use of a nested P...

Race, Choice and Richmond Public Schools: New Possibilities and Ongoing Challenges for Diversity in Urban Districts

ERIC Educational Resources Information Center

Siegel-Hawley, Genevieve

2014-01-01

Several contemporary demographic trends suggest that school systems in America's central cities, typically characterized by high levels of racial and economic isolation, are being presented with new opportunities to create quality, diverse schools. Still, numerous obstacles linger. Using multiple sources of data and innovative mapping tools, this…

Expressive Electronic Journal Writing: Freedom of Communication for Survivors of Acquired Brain Injury

ERIC Educational Resources Information Center

Fraas, Michael; Balz, Magdalen A.

2008-01-01

In addition to the impaired ability to effectively communicate, adults with acquired brain injury (ABI) also experience high incidences of depression, social isolation, and decreased quality of life. Expressive writing programs have been shown to be effective in alleviating these concomitant impairments in other populations including incarcerated…

Effect of RNA Integrity Determined With the Agilent 2100 Bioanalyzer on Bacterial RNA Quantification with RT-PCR

USDA-ARS?s Scientific Manuscript database

RNA integrity is critical for successful RNA quantification. The level of integrity required differs among sources and extraction procedures and has not been determined for bacterial RNA. Three RNA isolation methods were evaluated for their ability to produce high quality RNA from D. dadantii. The i...

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.

PubMed

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

Damping system for torsion modes of mirror isolation filters in TAMA300

NASA Astrophysics Data System (ADS)

Arase, Y.; Takahashi, R.; Arai, K.; Tatsumi, D.; Fukushima, M.; Yamazaki, T.; Fujimoto, Masa-Katsu; Agatsuma, K.; Nakagawa, N.

2008-07-01

The seismic attenuation system (SAS) in TAMA300 consists of a three-legged inverted pendulum and mirror isolation filters in order to provide a high level of seismic isolation. However, the mirror isolation filters have torsion modes with long decay time which disturb the interferometer operation for about half an hour if they get excited. In order to damp the torsion modes of the filters, we constructed a digital damping system using reflective photosensors with a large linear range. This system was installed to all of four SASs. By damping of the target torsion modes, the effective quality factors of the torsion modes are reduced to less than 10 or to unmeasurable level. This system is expected to reduce the inoperative period by the torsion mode excitation, and thus will contribute to improve the duty time of the gravitational wave detector.

Quantum Efficiency Loss after PID Stress: Wavelength Dependence on Cell Surface and Cell Edge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oh, Jaewon; Bowden, Stuart; TamizhMani, GovindaSamy

2015-06-14

It is known that the potential induced degradation (PID) stress of conventional p-base solar cells affects power, shunt resistance, junction recombination, and quantum efficiency (QE). One of the primary solutions to address the PID issue is a modification of chemical and physical properties of antireflection coating (ARC) on the cell surface. Depending on the edge isolation method used during cell processing, the ARC layer near the edges may be uniformly or non-uniformly damaged. Therefore, the pathway for sodium migration from glass to the cell junction could be either through all of the ARC surface if surface and edge ARC havemore » low quality or through the cell edge if surface ARC has high quality but edge ARC is defective due to certain edge isolation process. In this study, two PID susceptible cells from two different manufacturers have been investigated. The QE measurements of these cells before and after PID stress were performed at both surface and edge. We observed the wavelength dependent QE loss only in the first manufacturer's cell but not in the second manufacturer's cell. The first manufacturer's cell appeared to have low quality ARC whereas the second manufacturer's cell appeared to have high quality ARC with defective edge. To rapidly screen a large number of cells for PID stress testing, a new but simple test setup that does not require laminated cell coupon has been developed and is used in this investigation.« less

Fertilization rates and in vitro embryo production using sexed or non-sexed semen selected with a silane-coated silica colloid or Percoll.

PubMed

Rodríguez Villamil, P; Wei, H; Moreira, G; Caccia, M; Fernandez Taranco, M; Bó, G A

2012-07-01

The aim of this study was to evaluate sperm fertilization rates and in vitro embryo development rates for sexed and non-sexed semen selected using a silane-coated silica colloid method (Isolate) or Percoll. Frozen/thawed, sexed and unsexed semen samples from four Holstein bulls were randomly allocated to one of two different density gradient selection methods. Sperm quality (motility, concentration, morphology and membrane integrity) were evaluated and compared before and after sperm selection. Sperm motility and morphology improved (P < 0.005) after the sperm selection process with no differences between the two methods. For non-sexed semen, Percoll gradient increased the mean (± SEM) percentage of sperm recovered (57.3 ± 2.8) compared to Isolate (46.0 ± 1.8; P < 0.01). However, membrane integrity was higher after Isolate than Percoll (sexed semen: 41.0 ± 0.6 vs. 38.8 ± 0.8 and non-sexed semen 60.8 ± 1.6 vs. 58.8 ± 0.5; P < 0.05). The percentage of blastocysts produced was higher when either sexed or non-sexed semen was selected by Isolate (14.0 ± 1.0; 22.0 ± 1.1) than by Percoll (10.5 ± 1.5; 17.0 ± 2.1, respectively; P < 0.05). In summary, Isolate was a more effective method for the recovery of high quality sperm for in vitro fertilization embryo production. Copyright © 2012 Elsevier Inc. All rights reserved.

The Characterization of Chlorophyll-A and Microalgae Isolation Process of Wastewater Collected at Sembrong Dam

NASA Astrophysics Data System (ADS)

Wellson, R.; Othman, N.; Matias-Peralta, H. M.

2016-07-01

Recently, there has been an increasing number of river water quality deterioration that has brought into water quality disruptions that entering dams including in Johor and one of them is occurred in Sembrong Dam in Johor. Sembrong Dam is a major water source for some 120,000 people in the districts of Kluang and parts of Batu Pahat. The quality of water in Sembrong should be well-monitored in ensuring the continuous distribution of clean and safe water supply to peoples. Based on the news reported by The Star news dated on 11 May 2015, the water bodies in Sembrong Dam are polluted by the algae blooms which has started to cause problems in treating water phase by clogging up the filters and causing the production to be reduced and finally resulting in frequent water disruptions to residents. Therefore, there is a need to study the water quality of the dam water prior to further water treatment. One of important characterizations is by measuring chlorophyll-a and the isolation of the dominant microalgae species in the water body in which they are able to indicate the level of water pollution. This paper presents the determination of chlorophyll-a and the isolation of microalgae strains collected from Sembrong Dam. Chlorophyll-a is a photosynthetic pigment present in all species of phytoplankton, including algae and in some photosynthetic bacteria, known as cyanobacteria. The method used in measuring the chlorophyll-a is based on the standard method of IS0 10 260. The average chlorophyll-a concentration measured at Sembrong Dam is 175.9 µg L-1 and it is responsible for the appearance of green color in the sample and it is categorized into hypereutrophic state which is highly polluted. The technique used for isolation of microalgae strains is traditional method which is by spreading the sample on agar. The pure isolate indicated that the genus Botryococcus is the dominant algae species which is characterized morphologically. Both chlorophyll-a and microalgae isolation are good biological indicator that indicate the pollution of Sembrong Dam. The pure culture is very important that it can be used for further studies with series of different tests to understand its properties and character for sustainability approach towards environmentally friendly as well as for microalgae removal formula.

Improving methane yield and quality via co-digestion of cow dung mixed with food waste.

PubMed

Awasthi, Sanjeev Kumar; Joshi, Rutu; Dhar, Hiya; Verma, Shivpal; Awasthi, Mukesh Kumar; Varjani, Sunita; Sarsaiya, Surendra; Zhang, Zengqiang; Kumar, Sunil

2018-03-01

Methane (CH 4 ) production and quality were enhanced by the co-digestion of cow dung and food waste (FW) mixed with organic fraction of municipal solid waste (OFMSW) under optimized conditions in bench and semi continuous-scale mode for a period of 30 days. A bacterium capable of high yield of CH 4 was enriched and isolated by employing activated sewage sludge as the inoculums. The thirteen bacterial isolates were identified through morphological and biochemical tests. Gas chromatography was used to analyze the chemical compositions of the generated biogas. CH 4 yields were significantly higher during co-digestion of Run II (7.59 L) than Run I (3.7 L). Therefore, the co-digestion of FW with OFMSW and Run II was observed to be a competent method for biogas conversion from organic waste resources. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient method of protein extraction from Theobroma cacao L. roots for two-dimensional gel electrophoresis and mass spectrometry analyses.

PubMed

Bertolde, F Z; Almeida, A-A F; Silva, F A C; Oliveira, T M; Pirovani, C P

2014-07-04

Theobroma cacao is a woody and recalcitrant plant with a very high level of interfering compounds. Standard protocols for protein extraction were proposed for various types of samples, but the presence of interfering compounds in many samples prevented the isolation of proteins suitable for two-dimensional gel electrophoresis (2-DE). An efficient method to extract root proteins for 2-DE was established to overcome these problems. The main features of this protocol are: i) precipitation with trichloroacetic acid/acetone overnight to prepare the acetone dry powder (ADP), ii) several additional steps of sonication in the ADP preparation and extractions with dense sodium dodecyl sulfate and phenol, and iii) adding two stages of phenol extractions. Proteins were extracted from roots using this new protocol (Method B) and a protocol described in the literature for T. cacao leaves and meristems (Method A). Using these methods, we obtained a protein yield of about 0.7 and 2.5 mg per 1.0 g lyophilized root, and a total of 60 and 400 spots could be separated, respectively. Through Method B, it was possible to isolate high-quality protein and a high yield of roots from T. cacao for high-quality 2-DE gels. To demonstrate the quality of the extracted proteins from roots of T. cacao using Method B, several protein spots were cut from the 2-DE gels, analyzed by tandem mass spectrometry, and identified. Method B was further tested on Citrus roots, with a protein yield of about 2.7 mg per 1.0 g lyophilized root and 800 detected spots.

Rubber dam may increase the survival time of dental restorations.

PubMed

Keys, William; Carson, Susan J

2017-03-01

Data sourcesCochrane Oral Health's Trials Register, Cochrane Central Register of Controlled Trials (CENTRAL), Medline, Embase, LILACS, SciELO, Chinese BioMedical Literature Database, VIP, China National Knowledge Infrastructure, ClinicalTrials.gov, World Health Organization International Clinical Trials Registry Platform, OpenGrey and Sciencepaper Online databases. Handsearches in a number of journals.Study selectionRandomised controlled trials, including split-mouth studies assessing the effects of rubber dam isolation for restorative treatments in dental patients.Data extraction and synthesisTwo review authors independently screened the results of the electronic searches, extracted data and assessed the risk of bias of the included studies.ResultsFour studies involving a total of 1,270 patients were included. The studies were at high risk of bias. One trial was excluded from the analysis due to inconsistencies in the presented data. Restorations had a significantly higher survival rate in the rubber dam isolation group compared to the cotton roll isolation group at six months in participants receiving composite restorative treatment of non-carious cervical lesions (risk ratio (RR) 1.19, 95% confidence interval (CI) 1.04 to 1.37, very low-quality evidence). The rubber dam group had a lower risk of failure at two years in children undergoing proximal atraumatic restorative treatment in primary molars (hazard ratio (HR) 0.80, 95% CI 0.66 to 0.97, very low-quality evidence). One trial reported limited data showing that rubber dam usage during fissure sealing might shorten the treatment time. None of the included studies mentioned adverse effects or reported the direct cost of the treatment, or the level of patient acceptance/satisfaction. There was also no evidence evaluating the effects of rubber dam usage on the quality of the restorations.ConclusionsWe found some very low-quality evidence, from single studies, suggesting that rubber dam usage in dental direct restorative treatments may lead to a lower failure rate of the restorations, compared with the failure rate for cotton roll usage. Further high quality research evaluating the effects of rubber dam usage on different types of restorative treatments is required.

Detection of processed genetically modified food using CIM monolithic columns for DNA isolation.

PubMed

Jerman, Sergej; Podgornik, Ales; Cankar, Katarina; Cadet, Neza; Skrt, Mihaela; Zel, Jana; Raspor, Peter

2005-02-11

The availability of sufficient quantities of DNA of adequate quality is crucial in polymerase chain reaction (PCR)-based methods for genetically modified food detection. In this work, the suitability of anion-exchange CIM (Convective Interaction Media; BIA Separations, Ljubljana, Slovenia) monolithic columns for isolation of DNA from food was studied. Maize and its derivates corn meal and thermally pretreated corn meal were chosen as model food. Two commercially available CIM disk columns were tested: DEAE (diethylaminoethyl) and QA (quaternary amine). Preliminary separations were performed with standard solution of salmon DNA at different pH values and different NaCl concentrations in mobile phase. DEAE groups and pH 8 were chosen for further isolations of DNA from a complex matrix-food extract. The quality and quantity of isolated DNA were tested on agarose gel electrophoresis, with UV-scanning spectrophotometry, and by amplification with real-time PCR. DNA isolated in this way was of suitable quality for further PCR analyses. The described method is also applicable for DNA isolation from processed foods with decreased DNA content. Furthermore, it is more effective and less time-consuming in comparison with the existing proposed methods for isolation of DNA from plant-derived foods.

Comparison of the Microbial Quality of Lamb and Goat Meat Acquired from Internet and Local Retail Markets.

PubMed

Kim, Chyer; Stein, Roslyn A; Pao, Steven

2015-11-01

This study was conducted to evaluate the microbial quality of lamb and goat meat sold through local (Virginia) and Internet (U. S.) retail markets. A total of 134 frozen meat products consisting of locally purchased lamb ground (LLG) and lamb chops and Internet-procured lamb ground, goat ground, lamb chops (ILC), goat chops (IGC), lamb stew, and goat stew were tested. Significantly higher levels of aerobic mesophiles, psychrotrophs, and coliforms were found in the meat locally acquired than in the meat procured from the Internet. Similar average prevalence (27%) of Escherichia coli was observed regardless of market source. Ground meat had significantly high levels and prevalence of mesophiles, psychrotrophs, coliforms, and Listeria spp. One sample of LLG contained Campylobacter, and one sample of IGC contained Salmonella. Listeria spp. were present in 23 to 40% and 17 to 80% of samples from local and Internet markets, respectively. Pulsed-field gel electrophoresis (PFGE) of isolated E. coli strains revealed brand specificity and genomic diversity. No isolate from different brands and market sources had matching PFGE profiles. The average price of Internet meat ($23.4/kg) was about 1.2 times higher than the price of local meat, except for ILC, whose price was 2.7 times higher. This study revealed differences in microbial quality of lamb and goat meat based on market source; thus, meat products should be handled carefully regardless of market source because of the presence of high microbial levels and the high prevalence of pathogens.

A Quality Assessment Method Based on Common Distributed Targets for GF-3 Polarimetric SAR Data.

PubMed

Jiang, Sha; Qiu, Xiaolan; Han, Bing; Hu, Wenlong

2018-03-07

The GaoFen-3 (GF-3) satellite, launched on 10 August 2016, is the first C-band polarimetric synthetic aperture radar (PolSAR) satellite in China. The PolSAR system of GF-3 can collect a significant wealth of information for geophysical research and applications. Being used for related applications, GF-3 PolSAR images must be of good quality. It is necessary to evaluate the quality of polarimetric data and achieve the normalized quality monitoring during 8-year designed life of GF-3. In this study, a new quality assessment method of PolSAR data based on common distributed targets is proposed, and the performance of the method is analyzed by simulations and GF-3 experiments. We evaluate the quality of GF-3 PolSAR data by this method. Results suggest that GF-3 antenna is highly isolated, and the quality of calibrated data satisfies the requests of quantitative applications.

Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

PubMed Central

Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

2016-01-01

Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

Genotyping of Single Nucleotide Polymorphisms in DNA Isolated from Serum Using Sequenom MassARRAY Technology.

PubMed

Clendenen, Tess V; Rendleman, Justin; Ge, Wenzhen; Koenig, Karen L; Wirgin, Isaac; Currie, Diane; Shore, Roy E; Kirchhoff, Tomas; Zeleniuch-Jacquotte, Anne

2015-01-01

Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA. We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs) using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women's Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison. We observed that 60 of the 81 SNPs (74%) had high call frequencies (≥95%) using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95%) had highly concordant (>98%) genotype calls across all three sample types. High purity was not a critical factor to successful genotyping. Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies.

Water quality in three creeks in the backcountry of Grand Teton National Park, USA

USGS Publications Warehouse

Farag, A.M.; Goldstein, J.N.; Woodward, D.F.

2001-01-01

This study was conducted in Grand Teton National Park during the summers of 1996 and 1997 to investigate the water quality in two high human use areas: Garnet Canyon and lower Cascade Canyon. To evaluate the water quality in these creeks, fecal coliform, Giardia lamblia, coccidia, and microparticulates were measured in water samples. No evidence of fecal coliform, Giardia lamblia, or coccidia, was found in Garnet Creek. The water quality and general water chemistry of Garnet Creek was similar to the reference site. No Giardia lamblia or coccidia were found in Cascade Creek, but fecal coliforms were present. The isolated colonies of Escherichia coli from Cascade Creek matched the ribosome patterns of avian, deer, canine, elk, rodent, and human coliforms.

Characterization of airag collected in Ulaanbaatar, Mongolia with emphasis on isolated lactic acid bacteria.

PubMed

Choi, Suk-Ho

2016-01-01

Airag, alcoholic sour-tasting beverage, has been traditionally prepared by Mongolian nomads who naturally ferment fresh mares' milk. Biochemical and microbiological compositions of airag samples collected in Ulaanbaatar, Mongolia and physiological characteristics of isolated lactic acid bacteria were investigated. Protein composition and biochemical composition were determined using sodium dodecyl sulfate-gel electrophoresis and high performance liquid chromatography, respectively. Lactic acid bacteria were identified based on nucleotide sequence of 16S rRNA gene. Carbohydrate fermentation, acid survival, bile resistance and acid production in skim milk culture were determined. Equine whey proteins were present in airag samples more than caseins. The airag samples contained 0.10-3.36 % lactose, 1.44-2.33 % ethyl alcohol, 1.08-1.62 % lactic acid and 0.12-0.22 % acetic acid. Lactobacillus (L.) helveticus were major lactic acid bacteria consisting of 9 isolates among total 18 isolates of lactic acid bacteria. L. helveticus survived strongly in PBS, pH 3.0 but did not grow in MRS broth containing 0.1 % oxgall. A couple of L. helveticus isolates lowered pH of skim milk culture to less than 4.0 and produced acid up to more than 1.0 %. Highly variable biochemical compositions of the airag samples indicated inconsistent quality due to natural fermentation. Airag with low lactose content should be favorable for nutrition, considering that mares' milk with high lactose content has strong laxative effect. The isolates of L. helveticus which produced acid actively in skim milk culture might have a major role in production of airag.

Rubber dam isolation for restorative treatment in dental patients.

PubMed

Wang, Yan; Li, Chunjie; Yuan, He; Wong, May Cm; Zou, Jing; Shi, Zongdao; Zhou, Xuedong

2016-09-20

Successful restorations in dental patients depend largely on the effective control of moisture and microbes during the procedure. The rubber dam technique has been one of the most widely used isolation methods in dental restorative treatments. The evidence on the effects of rubber dam usage on the longevity of dental restorations is conflicting. Therefore, it is important to summarise the available evidence to determine the effects of this method. To assess the effects of rubber dam isolation compared with other types of isolation used for direct and indirect restorative treatments in dental patients. We searched the following electronic databases: Cochrane Oral Health's Trials Register (searched 17 August 2016), Cochrane Central Register of Controlled Trials (CENTRAL; 2016, Issue 7) in the Cochrane Library (searched 17 August 2016), MEDLINE Ovid (1946 to 17 August 2016), Embase Ovid (1980 to 17 August 2016), LILACS BIREME Virtual Health Library (Latin American and Caribbean Health Science Information database; 1982 to 17 August 2016), SciELO BIREME Virtual Health Library (1998 to 17 August 2016), Chinese BioMedical Literature Database (CBM, in Chinese) (1978 to 30 August 2016), VIP (in Chinese) (1989 to 30 August 2016), and China National Knowledge Infrastructure (CNKI, in Chinese) (1994 to 30 August 2016). We searched ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform, OpenGrey and Sciencepaper Online (in Chinese) for ongoing trials. There were no restrictions on the language or date of publication when searching the electronic databases. We included randomised controlled trials (including split-mouth trials) assessing the effects of rubber dam isolation for restorative treatments in dental patients. Two review authors independently screened the results of the electronic searches, extracted data and assessed the risk of bias of the included studies. We resolved disagreement by discussion. We included four studies that analysed 1270 participants (among which 233 participants were lost to follow-up). All the included studies were at high risk of bias. We excluded one trial from the analysis due to inconsistencies in the presented data.The results indicated that dental restorations had a significantly higher survival rate in the rubber dam isolation group compared to the cotton roll isolation group at six months in participants receiving composite restorative treatment of non-carious cervical lesions (risk ratio (RR) 1.19, 95% confidence interval (CI) 1.04 to 1.37, very low-quality evidence). It also showed that the rubber dam group had a lower risk of failure at two years in children undergoing proximal atraumatic restorative treatment in primary molars (hazard ratio (HR) 0.80, 95% CI 0.66 to 0.97, very low-quality evidence). One trial reported limited data showing that rubber dam usage during fissure sealing might shorten the treatment time. None of the included studies mentioned adverse effects or reported the direct cost of the treatment, or the level of patient acceptance/satisfaction. There was also no evidence evaluating the effects of rubber dam usage on the quality of the restorations. We found some very low-quality evidence, from single studies, suggesting that rubber dam usage in dental direct restorative treatments may lead to a lower failure rate of the restorations, compared with the failure rate for cotton roll usage. Further high quality research evaluating the effects of rubber dam usage on different types of restorative treatments is required.

Quality of red blood cells isolated from umbilical cord blood stored at room temperature.

PubMed

Zhurova, Mariia; Akabutu, John; Acker, Jason

2012-01-01

Red blood cells (RBCs) from cord blood contain fetal hemoglobin that is predominant in newborns and, therefore, may be more appropriate for neonatal transfusions than currently transfused adult RBCs. Post-collection, cord blood can be stored at room temperature for several days before it is processed for stem cells isolation, with little known about how these conditions affect currently discarded RBCs. The present study examined the effect of the duration cord blood spent at room temperature and other cord blood characteristics on cord RBC quality. RBCs were tested immediately after their isolation from cord blood using a broad panel of quality assays. No significant decrease in cord RBC quality was observed during the first 65 hours of storage at room temperature. The ratio of cord blood to anticoagulant was associated with RBC quality and needs to be optimized in future. This knowledge will assist in future development of cord RBC transfusion product.

Whole-Genome Sequencing of Lactobacillus salivarius Strains BCRC 14759 and BCRC 12574.

PubMed

Chiu, Shih-Hau; Chen, Chien-Chi; Wang, Li-Ting; Huang, Lina

2017-11-22

Lactobacillus salivarius BCRC 14759 has been identified as a high-exopolysaccharide-producing strain with potential as a probiotic or fermented dairy product. Here, we report the genome sequences of L. salivarius BCRC 14759 and the comparable strain BCRC 12574, isolated from human saliva. The PacBio RSII sequencing platform was used to obtain high-quality assemblies for characterization of this probiotic candidate. Copyright © 2017 Chiu et al.

Diversity and antibiograms of bacterial organisms isolated from samples of household drinking-water consumed by HIV-positive individuals in rural settings, South Africa.

PubMed

Samie, A; Mashao, M B; Bessong, P O; NKgau, T F; Momba, M N B; Obi, C L

2012-09-01

Diarrhoea is a hallmark of HIV infections in developing countries, and many diarrhoea-causing agents are often transmitted through water. The objective of the study was to determine the diversity and antibiotic susceptibility profiles of bacterial organisms isolated from samples of household drinking-water consumed by HIV-infected and AIDS patients. In the present study, household water stored for use by HIV-positive patients was tested for microbial quality, and isolated bacterial organisms were analyzed for their susceptibility profiles against 25 different antibiotics. The microbial quality of water was generally poor, and about 58% of water samples (n=270) were contaminated with faecal coliforms, with counts varying from 2 colony-forming unit (CFU)/100 mL to 2.4x10⁴ CFU/100 mL. Values of total coliform counts ranged from 17 CFU/100 mL to 7.9x10⁵/100 mL. In total, 37 different bacterial species were isolated, and the major isolates included Acinetobacter lwoffii (7.5%), Enterobacter cloacae (7.5%), Shigella spp. (14.2%), Yersinia enterocolitica (6.7%), and Pseudomonas spp. (16.3%). No Vibrio cholerae could be isolated; however, V. fluvialis was isolated from three water samples. The isolated organisms were highly resistant to cefazolin (83.5%), cefoxitin (69.2%), ampicillin (66.4%), and cefuroxime (66.2%). Intermediate resistance was observed against gentamicin (10.6%), cefepime (13.4%), ceftriaxone (27.6%), and cefotaxime (29.9%). Levofloxacin (0.7%), ceftazidime (2.2%), meropenem (3%), and ciprofloxacin (3.7%) were the most active antibiotics against all the microorganisms, with all recording less than 5% resistance. Multiple drug resistance was very common, and 78% of the organisms were resistant to three or more antibiotics. Education on treatment of household water is advised for HIV-positive patients, and measures should be taken to improve point-of-use water treatment as immunosuppressed individuals would be more susceptible to opportunistic infections.

Diversity and Antibiograms of Bacterial Organisms Isolated from Samples of Household Drinking-water Consumed by HIV-positive Individuals in Rural Settings, South Africa

PubMed Central

Mashao, M.B.; Bessong, P.O.; NKgau, T.F.; Momba, M.N.B.; Obi, C.L.

2012-01-01

Diarrhoea is a hallmark of HIV infections in developing countries, and many diarrhoea-causing agents are often transmitted through water. The objective of the study was to determine the diversity and antibiotic susceptibility profiles of bacterial organisms isolated from samples of household drinking-water consumed by HIV-infected and AIDS patients. In the present study, household water stored for use by HIV-positive patients was tested for microbial quality, and isolated bacterial organisms were analyzed for their susceptibility profiles against 25 different antibiotics. The microbial quality of water was generally poor, and about 58% of water samples (n=270) were contaminated with faecal coliforms, with counts varying from 2 colony-forming unit (CFU)/100 mL to 2.4×104 CFU/100 mL. Values of total coliform counts ranged from 17 CFU/100 mL to 7.9×105/100 mL. In total, 37 different bacterial species were isolated, and the major isolates included Acinetobacter lwoffii (7.5%), Enterobacter cloacae (7.5%), Shigella spp. (14.2%), Yersinia enterocolitica (6.7%), and Pseudomonas spp. (16.3%). No Vibrio cholerae could be isolated; however, V. fluvialis was isolated from three water samples. The isolated organisms were highly resistant to cefazolin (83.5%), cefoxitin (69.2%), ampicillin (66.4%), and cefuroxime (66.2%). Intermediate resistance was observed against gentamicin (10.6%), cefepime (13.4%), ceftriaxone (27.6%), and cefotaxime (29.9%). Levofloxacin (0.7%), ceftazidime (2.2%), meropenem (3%), and ciprofloxacin (3.7%) were the most active antibiotics against all the microorganisms, with all recording less than 5% resistance. Multiple drug resistance was very common, and 78% of the organisms were resistant to three or more antibiotics. Education on treatment of household water is advised for HIV-positive patients, and measures should be taken to improve point-of-use water treatment as immunosuppressed individuals would be more susceptible to opportunistic infections. PMID:23082625

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

PubMed

Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

2015-01-01

Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

Pectate lyase affects pathogenicity in natural isolates of Colletotrichum coccodes and in pelA gene-disrupted and gene-overexpressing mutant lines.

PubMed

Ben-Daniel, Bat-Hen; Bar-Zvi, Dudy; Tsror Lahkim, Leah

2012-02-01

Colletotrichum coccodes (Wallr.) S. Hughes, the causal agent of black dot on potato and anthracnose on tomato, reduces yield and crop quality. We explored the role of secreted pectate lyase (PL), a cell wall-degrading enzyme, in the aggressiveness of C. coccodes. In vitro-cultivated highly aggressive isolates secreted immunologically detectable PL levels 6 h after transfer to secondary medium versus 12 h for mildly aggressive isolates, suggesting that secreted PL is a virulence factor. The gene encoding PL, CcpelA, was cloned and used for the genetic manipulation of highly (US-41 and Si-72) and mildly (Si-60) aggressive isolates. CcpelA gene-disrupted mutants showed reduced aggressiveness towards tomato fruits and impaired PL secretion and extracellular activity. Conversely, overexpression of CcpelA in the Si-60 isolate increased its aggressiveness and PL secretion. Comparison of CcpelA cloned from isolates US-41 and Si-60 revealed that both encode identical proteins, but differ in their promoters. Bioinformatics analysis for cis-acting elements suggested that the promoters of the US-41 and Si-60 isolates contain one and no AreA-binding site (GATA box), respectively. AreA has been suggested to be involved in fungal aggressiveness; therefore, CcpelA may be a key virulence factor in C. coccodes pathogenicity, and the differences in isolate aggressiveness might result from promoter activity. Quantitative reverse transcriptase-polymerase chain reaction analyses confirmed the higher level of CcpelA transcript in isolate US-41 versus Si-60. © 2011 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2011 BSPP AND BLACKWELL PUBLISHING LTD.

The Broadband Quandary for Rural America. The Main Street Economist: Commentary on the Rural Economy.

ERIC Educational Resources Information Center

Staihr, Brian

High speed data services known as broadband have the potential to make rural areas less isolated and improve the rural quality of life, but physical barriers, sparse population density, and few markets present significant obstacles to their deployment in rural areas. Broadband applications such as e-commerce, distance education, and telemedicine…

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages.

PubMed

Esplin, Ian N D; Berg, Jordan A; Sharma, Ruchira; Allen, Robert C; Arens, Daniel K; Ashcroft, Cody R; Bairett, Shannon R; Beatty, Nolan J; Bickmore, Madeline; Bloomfield, Travis J; Brady, T Scott; Bybee, Rachel N; Carter, John L; Choi, Minsey C; Duncan, Steven; Fajardo, Christopher P; Foy, Brayden B; Fuhriman, David A; Gibby, Paul D; Grossarth, Savannah E; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A; Hurst, Emily; Hyde, Jonathan R; Ingersoll, Kayleigh; Jacobson, Caitlin M; James, Brady D; Jarvis, Todd M; Jaen-Anieves, Daniella; Jensen, Garrett L; Knabe, Bradley K; Kruger, Jared L; Merrill, Bryan D; Pape, Jenny A; Payne Anderson, Ashley M; Payne, David E; Peck, Malia D; Pollock, Samuel V; Putnam, Micah J; Ransom, Ethan K; Ririe, Devin B; Robinson, David M; Rogers, Spencer L; Russell, Kerri A; Schoenhals, Jonathan E; Shurtleff, Christopher A; Simister, Austin R; Smith, Hunter G; Stephenson, Michael B; Staley, Lyndsay A; Stettler, Jason M; Stratton, Mallorie L; Tateoka, Olivia B; Tatlow, P J; Taylor, Alexander S; Thompson, Suzanne E; Townsend, Michelle H; Thurgood, Trever L; Usher, Brittian K; Whitley, Kiara V; Ward, Andrew T; Ward, Megan E H; Webb, Charles J; Wienclaw, Trevor M; Williamson, Taryn L; Wells, Michael J; Wright, Cole K; Breakwell, Donald P; Hope, Sandra; Grose, Julianne H

2017-11-16

Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. Copyright © 2017 Esplin et al.

The White Working Class, Racism and Respectability: Victims, Degenerates and Interest-Convergence

ERIC Educational Resources Information Center

Gillborn, David

2010-01-01

This paper argues that race and class inequalities cannot be fully understood in isolation: their intersectional quality is explored through an analysis of how the White working class were portrayed in popular and political discourse during late 2008 (the timing is highly significant). While global capitalism reeled on the edge of financial…

A high proportion of NX-2 mycotoxin producing strains are found among Fusarium graminearum isolates from northeastern New York State

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum, a fungal pathogen of wheat, barley, and corn, produces a variety of trichothecene mycotoxins that are important as aggressiveness factors and as seed contaminants reducing grain quality. A previous survey of the pathogen in New York State identified variation in genes indicativ...

Apparatus and method for laser velocity interferometry

DOEpatents

Stanton, Philip L.; Sweatt, William C.; Crump, Jr., O. B.; Bonzon, Lloyd L.

1993-09-14

An apparatus and method for laser velocity interferometry employing a fixed interferometer cavity and delay element. The invention permits rapid construction of interferometers that may be operated by those non-skilled in the art, that have high image quality with no drift or loss of contrast, and that have long-term stability even without shock isolation of the cavity.

Rethinking the history of common walnut (Juglans regia L.) in Europe: Its origins and human interactions

Treesearch

Paola Pollegioni; Keith Woeste; Francesca Chiocchini; Stefano Del Lungo; Marco Ciolfi; Irene Olimpieri; Virginia Tortolano; Jo Clark; Gabriel E. Hemery; Sergio Mapelli; Maria Emilia Malvolti; Tzen-Yuh Chiang

2017-01-01

Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its high-quality wood and nuts. It is generally accepted that after the last glaciation J. regia survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new...

Spermatozoa input concentrations and RNA isolation methods on RNA yield and quality in bull (Bos taurus).

PubMed

Parthipan, Sivashanmugam; Selvaraju, Sellappan; Somashekar, Lakshminarayana; Kolte, Atul P; Arangasamy, Arunachalam; Ravindra, Janivara Parameswaraiah

2015-08-01

Sperm RNA can be used to understand the past spermatogenic process, future successful fertilization, and embryo development. To study the sperm RNA composition and function, isolation of good quality RNA with sufficient quantity is essential. The objective of this study was to assess the influence of sperm input concentrations and RNA isolation methods on RNA yield and quality in bull sperm. The fresh semen samples from bulls (n = 6) were snap-frozen in liquid nitrogen and stored at -80 °C. The sperm RNA was isolated using membrane-based methods combined with TRIzol (RNeasy+TRIzol and PureLink+TRIzol) and conventional methods (TRIzol, Double TRIzol, and RNAzol RT). Based on fluorometric quantification, combined methods resulted in significantly (P < 0.05) higher total RNA yields (800-900 ng/30-40 × 10(6)) as compared with other methods and yielded 20 to 30 fg of RNA/spermatozoon. The quality of RNA isolated by membrane-based methods was superior to that isolated by conventional methods. The sperm RNA was observed to be intact as well as fragmented (50-2000 bp). The study revealed that the membrane-based methods with a cocktail of lysis solution and an optimal input concentration of 30 to 40 million sperm were optimal for maximum recovery of RNA from bull spermatozoa. Copyright © 2015 Elsevier Inc. All rights reserved.

Interlaboratory Study of Quality Control Isolates for a Broth Microdilution Method (Modified CLSI M38-A) for Testing Susceptibilities of Dermatophytes to Antifungals▿

PubMed Central

Ghannoum, M. A.; Arthington-Skaggs, B.; Chaturvedi, V.; Espinel-Ingroff, A.; Pfaller, M. A.; Rennie, R.; Rinaldi, M. G.; Walsh, T. J.

2006-01-01

The Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards, or NCCLS) M38-A standard for the susceptibility testing of filamentous fungi does not specifically address the testing of dermatophytes. In 2003, a multicenter study investigated the reproducibility of the microdilution method developed at the Center for Medical Mycology, Cleveland, Ohio, for testing the susceptibility of dermatophytes. Data from that study supported the introduction of this method for testing dermatophytes in the future version of the CLSI M38-A standard. In order for the method to be accepted by CLSI, appropriate quality control isolates needed to be identified. To that end, an interlaboratory study, involving the original six laboratories plus two additional sites, was conducted to evaluate potential candidates for quality control isolates. These candidate strains included five Trichophyton rubrum strains known to have elevated MICs to terbinafine and five Trichophyton mentagrophytes strains. Antifungal agents tested included ciclopirox, fluconazole, griseofulvin, itraconazole, posaconazole, terbinafine, and voriconazole. Based on the data generated, two quality control isolates, one T. rubrum isolate and one T. mentagrophytes isolate, were identified and submitted to the American Type Culture Collection (ATCC) for inclusion as reference strains. Ranges encompassing 95.2 to 97.9% of all data points for all seven drugs were established. PMID:17050812

Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa.

PubMed

Ekwanzala, Mutshiene Deogratias; Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Keshri, Jitendra; Momba, Ndombo Benteke Maggy

2017-12-01

To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r 2 values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r 2 values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.

Overview of the ISOL facility for the RISP

NASA Astrophysics Data System (ADS)

Woo, H. J.; Kang, B. H.; Tshoo, K.; Seo, C. S.; Hwang, W.; Park, Y.-H.; Yoon, J. W.; Yoo, S. H.; Kim, Y. K.; Jang, D. Y.

2015-02-01

The key feature of the Isotope Separation On-Line (ISOL) facility is its ability to provide high-intensity and high-quality beams of neutron-rich isotopes with masses in the range of 80-160 by means of a 70-MeV proton beam directly impinging on uranium-carbide thin-disc targets to perform forefront research in nuclear structure, nuclear astrophysics, reaction dynamics and interdisciplinary fields like medical, biological and material sciences. The technical design of the 10-kW and the 35-kW direct fission targets with in-target fission rates of up to 1014 fissions/s has been finished, and for the development of the ISOL fission-target chemistry an initial effort has been made to produce porous lanthanum-carbide (LaCx) discs as a benchmark for the final production of porous UCx discs. For the production of various beams, three classes of ion sources are under development at RISP (Rare Isotope Science Project), the surface ion source, the plasma ion source (FEBIAD), the laser ion source, and the engineering design of the FEBIAD is in progress for prototype fabrication. The engineering design of the ISOL target/ion source front-end system is also in progress, and a prototype will be used for an off-line test facility in front of the pre-separator. The technical designs of other basic elements at the ISOL facility, such as the RF-cooler, the high-resolution mass separator, and the A/q separator, have been finished, and the results, along with the future plans, are introduced.

Demographic, clinical, and quality of life variables related to embarrassment in veterans living with an intestinal stoma.

PubMed

Mitchell, Kimberly A; Rawl, Susan M; Schmidt, C Max; Grant, Marcia; Ko, Clifford Y; Baldwin, Carol M; Wendel, Christopher; Krouse, Robert S

2007-01-01

The study aims were to identify demographic, clinical, and quality of life variables related to embarrassment for people living with ostomies and to determine the experiences and/or feelings of veterans who were embarrassed by their ostomy. This was a cross-sectional, correlational study. A convenience sample of veterans (n = 239) living with ostomies from 3 VA medical centers was studied. The veterans were primarily Caucasian (84%), male (92%), and older (M = 69). The modified City of Hope Quality of Life-Ostomy questionnaire was used. Additionally, an open-ended question related to living with an ostomy was asked. The questionnaire packets were mailed to participants and self-administered. Approximately half of the participants (48%) rated their embarrassment as low, but 26% reported high embarrassment. Participants with high embarrassment were compared to those with low embarrassment on demographic, clinical, and quality of life variables. High embarrassment was associated with poorer total quality of life (P < .001) and poorer quality of life on the physical (P < .001), psychological (P < .001), social (P < .001), and spiritual (P < .001) subscales. Younger (P < .001) and unpartnered veterans (P < .001) were more likely to be highly embarrassed. Veterans with high embarrassment had higher anxiety (P < .001) and depression (P < .001), more difficulty with intimacy (P < .001), and felt more isolated (P < .001). Spiritual domain variables like hopefulness were associated with low embarrassment (P < .001). Sources of embarrassment included leakage, odor, and noise. Embarrassment may negatively impact a person's quality of life; therefore, the variables associated with high embarrassment should be recognized and addressed.

Oleaginous Microalgae from Dairy Farm Wastewater for Biodiesel Production: Isolation, Characterization and Mass Cultivation.

PubMed

Sun, Zheng; Fang, Xiao-Peng; Li, Xiao-Yang; Zhou, Zhi-Gang

2018-02-01

Producing biodiesel from microalgae grown in wastewater is environment-friendly and cost-effective. The present study investigated the algae found in wastewater of a local dairy farm for their potential as biodiesel feedstocks. Thirteen native algal strains were isolated. On the basis of morphology and 16S/18S rRNA gene sequences, one strain was identified to be a member of cyanobacteria, while other 12 strains belong to green algae. After screening, two Scenedesmus strains out of the 13 microalgae isolates demonstrated superiority in growth rate, lipid productivity, and sedimentation properties, and therefore were selected for further scale-up outdoor cultivation. Both Scenedesmus strains quickly adapted to the outdoor conditions, exhibiting reasonably good growth and strong anti-contamination capabilities. In flat-plate photobioreactors (PBRs), algal cells accumulated predominantly neutral lipids that accounted for over 60% of total lipids with almost 70% being triacylglycerol. In addition, Scenedesmus obliquus had a high content of monounsaturated fatty acids, of which the amount of oleic acid (C18:1) was up to 27.11%. Based on these findings, the dairy farm wastewater-isolated Scenedesmus strains represent promising sources of low-cost, high-quality oil for biofuel production.

Screening of Functional Rhizopus stolonifer for Alcohol Fermentation and Production of High Quality Korean Traditional Rice Wine

PubMed Central

Song, Jung-Hwa; Kim, Jae-Ho; Ahn, Byung-Hak

2010-01-01

Different strains of mold were screened for the production of high quality Korean traditional rice wine with anti-hypertension and good acceptability. We isolated 867 nuruk mold strains and selected 24 for further study based on measurement of amylase activity. Among them, mold No. 17 showed high ethanol production upon fermentation with Saccharomyces cerevisiae as well as anti-hypertensive properties. The No. 17 strain was therefore selected as the functional mold and later identified as Rhizopus stolonifer based on molecular biological characteristics. Optimal fermentation conditions for the brewing of anti-hypertensive traditional rice wine comprised the addition of R. stolonifer No. 17 koji at a concentration of 35 sp/g and a fermentation period of 10 days at 25℃ using S. cerevisiae. PMID:23956639

Screening of Functional Rhizopus stolonifer for Alcohol Fermentation and Production of High Quality Korean Traditional Rice Wine.

PubMed

Song, Jung-Hwa; Kim, Jae-Ho; Ahn, Byung-Hak; Lee, Jong-Soo

2010-06-01

Different strains of mold were screened for the production of high quality Korean traditional rice wine with anti-hypertension and good acceptability. We isolated 867 nuruk mold strains and selected 24 for further study based on measurement of amylase activity. Among them, mold No. 17 showed high ethanol production upon fermentation with Saccharomyces cerevisiae as well as anti-hypertensive properties. The No. 17 strain was therefore selected as the functional mold and later identified as Rhizopus stolonifer based on molecular biological characteristics. Optimal fermentation conditions for the brewing of anti-hypertensive traditional rice wine comprised the addition of R. stolonifer No. 17 koji at a concentration of 35 sp/g and a fermentation period of 10 days at 25℃ using S. cerevisiae.

Ground-water quality atlas of Wisconsin

USGS Publications Warehouse

Kammerer, Phil A.

1981-01-01

This report summarizes data on ground-water quality stored in the U.S. Geological Survey's computer system (WATSTORE). The summary includes water quality data for 2,443 single-aquifer wells, which tap one of the State's three major aquifers (sand and gravel, Silurian dolomite, and sandstone). Data for dissolved solids, hardness, alkalinity, calcium, magnesium, sodium, potassium, iron, manganese, sulfate, chloride, fluoride, and nitrate are summarized by aquifer and by county, and locations of wells for which data are available 1 are shown for each aquifer. Calcium, magnesium, and bicarbonate (the principal component of alkalinity) are the major dissolved constituents in Wisconsin's ground water. High iron concentrations and hardness cause ground-water quality problems in much of the State. Statewide ,summaries of trace constituent (selected trace metals; arsenic, boron, and organic carbon) concentrations show that these constituents impair water quality in only a few isolated wells.

Phenotypic and Genotypic Characterization of Non-Starter Lactic Acid Bacteria in Mature Cheddar Cheese

PubMed Central

Fitzsimons, N. A.; Cogan, T. M.; Condon, S.; Beresford, T.

1999-01-01

Non-starter lactic acid bacteria were isolated from 14 premium-quality and 3 sensorially defective mature Irish Cheddar cheeses, obtained from six manufacturers. From countable plates of Lactobacillus-selective agar, 20 single isolated colonies were randomly picked per cheese. All 331 viable isolates were biochemically characterized as mesophilic (i.e., group II) Lactobacillus spp. Phenotypically, the isolates comprised 96.4% L. paracasei, 2.1% L. plantarum, 0.3% L. curvatus, 0.3% L. brevis, and 0.9% unidentified species. Randomly amplified polymorphic DNA (RAPD) analysis was used to rapidly identify the dominant strain groups in nine cheeses from three of the factories, and through clustering by the unweighted pair group method with arithmetic averages, an average of seven strains were found per cheese. In general, strains isolated from cheese produced at the same factory clustered together. The majority of isolates associated with premium-quality cheese grouped together and apart from clusters of strains from defective-quality cheese. No correlation was found between the isomer of lactate produced and RAPD profiles, although isolates which did not ferment ribose clustered together. The phenotypic and genotypic methods employed were validated with a selection of 31 type and reference strains of mesophilic Lactobacillus spp. commonly found in Cheddar cheese. RAPD analysis was found to be a useful and rapid method for identifying isolates to the species level. The low homology exhibited between RAPD banding profiles for cheese isolates and collection strains demonstrated the heterogeneity of the L. paracasei complex. PMID:10427029

Quality improvement and geographical indication of cachaça (Brazilian spirit) by using locally selected yeast strains.

PubMed

Barbosa, E A; Souza, M T; Diniz, R H S; Godoy-Santos, F; Faria-Oliveira, F; Correa, L F M; Alvarez, F; Coutrim, M X; Afonso, R J C F; Castro, I M; Brandão, R L

2016-10-01

In order to improve the quality and to create a biological basis for obtainment of the protected denomination of origin (PDO), indigenous yeast were isolated and characterized for use in Salinas city (the Brazilian region of quality cachaça production). Seven thousand and two hundred yeast colonies from 15 Salinas city distilleries were screened based on their fermentative behaviour and the physicochemical composition of cachaça. Molecular polymorphic analyses were performed to characterize these isolates. Two Saccharomyces cerevisiae strains (nos. 678 and 680) showed appropriate characteristics to use in the cachaça production: low levels of acetaldehyde and methanol, and high ethyl lactate/ethyl acetate ratio respectively. They also presented polymorphic characteristics more closely related between themselves even when compared to other strains from Salinas. The application of selected yeast to cachaça production can contribute for the improvement of the quality product as well as be used as a natural marker for PDO. This study suggests that the use of selected yeast strains could contribute to obtain a cachaça similar to those produced traditionally, while getting wide acceptation in the market, yet presenting more homogeneous organoleptic characteristics, and thus contributing to the PDO implementation. © 2016 The Society for Applied Microbiology.

Phenotypic and molecular detection of the bla KPC gene in clinical isolates from inpatients at hospitals in São Luis, MA, Brazil.

PubMed

Ribeiro, Patricia Cristina Saldanha; Monteiro, Andrea Souza; Marques, Sirlei Garcia; Monteiro, Sílvio Gomes; Monteiro-Neto, Valério; Coqueiro, Martina Márcia Melo; Marques, Ana Cláudia Garcia; de Jesus Gomes Turri, Rosimary; Santos, Simone Gonçalves; Bomfim, Maria Rosa Quaresma

2016-12-07

Bacteria that produce Klebsiella pneumoniae carbapenemases (KPCs) are resistant to broad-spectrum β-lactam antibiotics. The objective of this study was to phenotypically and genotypically characterize the antibiotic susceptibility to carbapenems of 297 isolates recovered from clinical samples obtained from inpatients at 16 hospitals in São Luis (Maranhão, Brazil). The study was conducted using phenotypic tests and molecular methods, including polymerase chain reaction (PCR), sequencing and enterobacterial repetitive intergenic consensus (ERIC)-PCR. The nonparametric chi-square test of independence was used to evaluate the associations between the bacterial bla KPC gene and the modified Hodge test, and the chi-square adherence test was used to assess the frequency of carbapenemases and their association with the bla KPC gene. The most frequently isolated species were Acinetobacter baumannii (n = 128; 43.0%), K. pneumoniae (n = 75; 25.2%), and Pseudomonas aeruginosa (n = 42; 14.1%). Susceptibility assays showed that polymixin B was active against 89.3% of the bacterial isolates. The Acinetobacter spp. and K. pneumoniae strains were susceptible to amikacin and tigecycline, and Pseudomonas spp. were sensitive to gentamicin and amikacin. Among the 297 isolates, 100 (33.7%) were positive for the bla KPC gene, including non-fermentative bacteria (A. baumannii) and Enterobacteriaceae species. Among the isolates positive for the bla KPC gene, K. pneumoniae isolates had the highest positivity rate of 60.0%. The bla KPC gene variants detected included KPC-2, which was found in all isolates belonging to species of the Enterobacteriaceae family. KPC-2 and KPC-3 were observed in A. baumannii isolates. Importantly, the bla KPC gene was also detected in three Raoultella isolates and one isolate of the Pantoea genus. ERIC-PCR patterns showed a high level of genetic diversity among the bacterial isolates; it was capable of distinguishing 34 clones among 100 strains that were positive for bla KPC and were circulating in 11 of the surveyed hospitals. The high frequency of the bla KPC gene and the high degree of clonal diversity among microorganisms isolated from patients from different hospitals in São Luis suggest the need to improve the quality of health care to reduce the incidence of infections and the emergence of carbapenem resistance in these bacteria as well as other Gram-negative pathogens.

Distribution and Validation of CERES Irradiance Global Data Products Via Web Based Tools

NASA Technical Reports Server (NTRS)

Rutan, David; Mitrescu, Cristian; Doelling, David; Kato, Seiji

2016-01-01

The CERES SYN1deg product provides climate quality 3-hourly globally gridded and temporally complete maps of top of atmosphere, in atmosphere, and surface fluxes. This product requires efficient release to the public and validation to maintain quality assurance. The CERES team developed web-tools for the distribution of both the global gridded products and grid boxes that contain long term validation sites that maintain high quality flux observations at the Earth's surface. These are found at: http://ceres.larc.nasa.gov/order_data.php. In this poster we explore the various tools available to users to sub-set, download, and validate using surface observations the SYN1Deg and Surface-EBAF products. We also analyze differences found in long-term records from well-maintained land surface sites such as the ARM central facility and high quality buoy radiometers, which due to their isolated nature cannot be maintained in a similar manner to their land based counterparts.

Habitat quality mediates personality through differences in social context.

PubMed

Belgrad, Benjamin A; Griffen, Blaine D

2017-06-01

Assessing the stability of animal personalities has become a major goal of behavioral ecologists. Most personality studies have utilized solitary individuals, but little is known on the extent that individuals retain their personality across ecologically relevant group settings. We conducted a field survey which determined that mud crabs, Panopeus herbstii, remain scattered as isolated individuals on degraded oyster reefs while high quality reefs can sustain high crab densities (>10 m -2 ). We examined the impact of these differences in social context on personality by quantifying the boldness of the same individual crabs when in isolation and in natural cohorts. Crabs were also exposed to either a treatment of predator cues or a control of no cue throughout the experiment to assess the strength of this behavioral reaction norm. Crabs were significantly bolder when in groups than as solitary individuals with predator cue treatments exhibiting severally reduced crab activity levels in comparison to corresponding treatments with no predator cues. Behavioral plasticity depended on the individual and was strongest in the presence of predator cues. While bold crabs largely maintained their personality in isolation and group settings, shy crabs would become substantially bolder when among conspecifics. These results imply that the shifts in crab boldness were a response to changes in perceived predation risk, and provide a mechanism for explaining variation in behavioral plasticity. Such findings suggest that habitat degradation may produce subpopulations with different behavioral patterns because of differing social interactions between individual animals.

High-quality draft genome sequence of Effusibacillus lacus strain skLN1T, facultative anaerobic spore-former isolated from freshwater lake sediment.

PubMed

Watanabe, Miho; Tokizawa, Riho; Kojima, Hisaya; Fukui, Manabu

2017-01-01

10.1601/nm.25721 strain skLN1 T is the type strain of the type species in the genus 10.1601/nm.25720 which is the one of the genera in the family 10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain skLN1 T is a Gram-positive, spore-forming thermophilic neutrophile isolated from freshwater lake sediment. Here, we present the draft genome sequence of strain skLN1 T , which consists of 3,902,380 bp with a G + C content of 50.38%.

Isolation and amplification of genomic DNA from recalcitrant dried berries of black pepper (Piper nigrum L.)--a medicinal spice.

PubMed

Dhanya, K; Kizhakkayil, Jaleel; Syamkumar, S; Sasikumar, B

2007-10-01

Black pepper is an important medicinal spice traded internationally. The extraction of high quality genomic DNA for PCR amplification from dried black pepper is challenging because of the presence of the exceptionally large amount of oxidized polyphenolic compounds, polysaccharides and other secondary metabolites. Here we report a modified hexadecyl trimethyl ammonium bromide (CTAB) protocol by incorporating potassium acetate and a final PEG precipitation step to isolate PCR amplifiable genomic DNA from dried and powdered berries of black pepper. The protocol has trade implication as it will help in the PCR characterization of traded black peppers from different countries.

No-migration variance petition. Appendices C--J: Volume 5, Revision 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1990-03-01

Volume V contains the appendices for: closure and post-closure plans; RCRA ground water monitoring waver; Waste Isolation Division Quality Program Manual; water quality sampling plan; WIPP Environmental Procedures Manual; sample handling and laboratory procedures; data analysis; and Annual Site Environmental Monitoring Report for the Waste Isolation Pilot Plant.

Sn-doped Bi 1.1Sb 0.9Te 2S bulk crystal topological insulator with excellent properties

DOE PAGES

S. K. Kushwaha; Pletikosic, I.; Liang, T.; ...

2016-04-27

A long-standing issue in topological insulator research has been to find a bulk single crystal material that provides a high quality platform for characterizing topological surface states without interference from bulk electronic states. This material would ideally be a bulk insulator, have a surface state Dirac point energy well isolated from the bulk valence and conduction bands, display quantum oscillations from the surface state electrons, and be growable as large, high quality bulk single crystals. Here we show that this materials obstacle is overcome by bulk crystals of lightly Sn-doped Bi 1.1Sb 0.9Te 2S grown by the Vertical Bridgeman method.more » We characterize Sn-BSTS via angle-resolved photoemission spectroscopy, scanning tunneling microscopy, transport studies, X-ray diffraction, and Raman scattering. We present this material as a high quality topological insulator that can be reliably grown as bulk single crystals and thus studied by many researchers interested in topological surface states.« less

Fungal isolates from a Pu-erh type tea fermentation and their ability to convert tea polyphenols to theabrownins.

PubMed

Wang, Qiuping; Gong, Jiashun; Chisti, Yusuf; Sirisansaneeyakul, Sarote

2015-04-01

The natural microbiota involved in the fermentation influence the quality and taste of fully postfermented teas such as China's Pu-erh tea. Ten microbial isolates representing 6 species were recovered from a solid-state fermentation of a Pu-erh type tea. The isolates were Aspergillus tubingensis, Aspergillus marvanovae, Rhizomucor pusillus, Rhizomucor tauricus, Aspergillus fumigatus, and Candida mogii. With the exception of A. marvanovae and C. mogii, all these microorganisms have been previously reported in solid-state fermentations of native Pu-erh tea. The ability of the isolates for converting the tea polyphenols to bioactive theabrownins in infusions of sun-dried green tea leaves in a submerged fermentation process was subsequently investigated. All isolates except C. mogii TISTR 5938 effectively produced theabrownins in a 4-d fermentation in shake flasks at 40 °C, 250 rpm. A. tubingensis TISTR 3646, A. tubingensis TISTR 3647, A. marvanovae TISTR 3648, and A. fumigatus TISTR 3654 produced theabrownins at particularly high levels of 6.5, 12.4, 11.1, and 8.4 g/L, respectively. © 2015 Institute of Food Technologists®

Islet product characteristics and factors related to successful human islet transplantation from the Collaborative Islet Transplant Registry (CITR) 1999-2010.

PubMed

Balamurugan, A N; Naziruddin, B; Lockridge, A; Tiwari, M; Loganathan, G; Takita, M; Matsumoto, S; Papas, K; Trieger, M; Rainis, H; Kin, T; Kay, T W; Wease, S; Messinger, S; Ricordi, C; Alejandro, R; Markmann, J; Kerr-Conti, J; Rickels, M R; Liu, C; Zhang, X; Witkowski, P; Posselt, A; Maffi, P; Secchi, A; Berney, T; O'Connell, P J; Hering, B J; Barton, F B

2014-11-01

The Collaborative Islet Transplant Registry (CITR) collects data on clinical islet isolations and transplants. This retrospective report analyzed 1017 islet isolation procedures performed for 537 recipients of allogeneic clinical islet transplantation in 1999-2010. This study describes changes in donor and islet isolation variables by era and factors associated with quantity and quality of final islet products. Donor body weight and BMI increased significantly over the period (p<0.001). Islet yield measures have improved with time including islet equivalent (IEQ)/particle ratio and IEQs infused. The average dose of islets infused significantly increased in the era of 2007-2010 when compared to 1999-2002 (445.4±156.8 vs. 421.3±155.4×0(3) IEQ; p<0.05). Islet purity and total number of β cells significantly improved over the study period (p<0.01 and <0.05, respectively). Otherwise, the quality of clinical islets has remained consistently very high through this period, and differs substantially from nonclinical islets. In multivariate analysis of all recipient, donor and islet factors, and medical management factors, the only islet product characteristic that correlated with clinical outcomes was total IEQs infused. This analysis shows improvements in both quantity and some quality criteria of clinical islets produced over 1999-2010, and these parallel improvements in clinical outcomes over the same period. © 2014 The Authors. American Journal of Transplantation Published by Wiley Periodicals, Inc. on behalf of American Society of Transplant Surgeons.

Islet Product Characteristics and Factors Related to Successful Human Islet Transplantation From the Collaborative Islet Transplant Registry (CITR) 1999–2010

PubMed Central

Balamurugan, A N; Naziruddin, B; Lockridge, A; Tiwari, M; Loganathan, G; Takita, M; Matsumoto, S; Papas, K; Trieger, M; Rainis, H; Kin, T; Kay, T W; Wease, S; Messinger, S; Ricordi, C; Alejandro, R; Markmann, J; Kerr-Conti, J; Rickels, M R; Liu, C; Zhang, X; Witkowski, P; Posselt, A; Maffi, P; Secchi, A; Berney, T; O’Connell, P J; Hering, B J; Barton, F B

2014-01-01

The Collaborative Islet Transplant Registry (CITR) collects data on clinical islet isolations and transplants. This retrospective report analyzed 1017 islet isolation procedures performed for 537 recipients of allogeneic clinical islet transplantation in 1999–2010. This study describes changes in donor and islet isolation variables by era and factors associated with quantity and quality of final islet products. Donor body weight and BMI increased significantly over the period (p < 0.001). Islet yield measures have improved with time including islet equivalent (IEQ)/particle ratio and IEQs infused. The average dose of islets infused significantly increased in the era of 2007–2010 when compared to 1999–2002 (445.4 ± 156.8 vs. 421.3 ± 155.4 ×103 IEQ; p < 0.05). Islet purity and total number of β cells significantly improved over the study period (p < 0.01 and <0.05, respectively). Otherwise, the quality of clinical islets has remained consistently very high through this period, and differs substantially from nonclinical islets. In multivariate analysis of all recipient, donor and islet factors, and medical management factors, the only islet product characteristic that correlated with clinical outcomes was total IEQs infused. This analysis shows improvements in both quantity and some quality criteria of clinical islets produced over 1999–2010, and these parallel improvements in clinical outcomes over the same period. PMID:25278159

Racial residential segregation and preterm birth: built environment as a mediator.

PubMed

Anthopolos, Rebecca; Kaufman, Jay S; Messer, Lynne C; Miranda, Marie Lynn

2014-05-01

Racial residential segregation has been associated with preterm birth. Few studies have examined mediating pathways, in part because, with binary outcomes, indirect effects estimated from multiplicative models generally lack causal interpretation. We develop a method to estimate additive-scale natural direct and indirect effects from logistic regression. We then evaluate whether segregation operates through poor-quality built environment to affect preterm birth. To estimate natural direct and indirect effects, we derive risk differences from logistic regression coefficients. Birth records (2000-2008) for Durham, North Carolina, were linked to neighborhood-level measures of racial isolation and a composite construct of poor-quality built environment. We decomposed the total effect of racial isolation on preterm birth into direct and indirect effects. The adjusted total effect of an interquartile increase in racial isolation on preterm birth was an extra 27 preterm events per 1000 births (risk difference = 0.027 [95% confidence interval = 0.007 to 0.047]). With poor-quality built environment held at the level it would take under isolation at the 25th percentile, the direct effect of an interquartile increase in isolation was 0.022 (-0.001 to 0.042). Poor-quality built environment accounted for 35% (11% to 65%) of the total effect. Our methodology facilitates the estimation of additive-scale natural effects with binary outcomes. In this study, the total effect of racial segregation on preterm birth was partially mediated by poor-quality built environment.

High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha

Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. Lastly, the 7,679,067 bp high-quality permanent draft genome is arrangedmore » in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha

We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs,more » contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).« less

High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T

DOE PAGES

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha; ...

2015-09-19

Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. Lastly, the 7,679,067 bp high-quality permanent draft genome is arrangedmore » in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

DOE PAGES

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha; ...

2015-10-16

We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs,more » contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).« less

Antibiotic resistant airborne bacteria and their multidrug resistance pattern at University teaching referral Hospital in South Ethiopia.

PubMed

Solomon, Fithamlak Bisetegen; Wadilo, Fiseha Wada; Arota, Amsalu Amache; Abraham, Yishak Leka

2017-04-12

Hospitals provide a reservoir of microorganisms, many of which are multi-resistant to antibiotics. Emergence of multi-drug resistant strains in a hospital environment, particularly in developing countries is an increasing problem to infection treatment. This study aims at assessing antibiotic resistant airborne bacterial isolates. A cross-sectional study was conducted at Wolaita Sodo university teaching and referral Hospital. Indoor air samples were collected by using passive air sampling method. Sample processing and antimicrobial susceptibility testing were done following standard bacteriological techniques. The data was analyzed using SPSS version 20. Medically important bacterial pathogens, Coagulase negative staphylococci (29.6%), Staphylococcus aureus (26.3%), Enterococci species, Enterococcus faecalis and Enterococcus faecium (16.5%), Acinetobacter species (9.5%), Escherichia coli (5.8%) and Pseudomonas aeruginosa (5.3%) were isolated. Antibiotic resistance rate ranging from 7.5 to 87.5% was detected for all isolates. Acinetobacter species showed a high rate of resistance for trimethoprim-sulfamethoxazole, gentamicin (78.2%) and ciprofloxacin (82.6%), 28 (38.9%) of S. aureus isolates were meticillin resistant, and 7.5% Enterococci isolates of were vancomycin resistant. 75.3% of all bacterial pathogen were multi-drug resistant. Among them, 74.6% were gram positive and 84% were gram negative. Multi-drug resistance were observed among 84.6% of P. aeruginosa, of 82.5% Enterococcii, E. coli 78.6%, S. aureus 76.6%, and Coagulase negative staphylococci of 73.6%. Indoor environment of the hospital was contaminated with airborne microbiotas, which are common cause of post-surgical site infection in the study area. Bacterial isolates were highly resistant to commonly used antibiotics with high multi-drug resistance percentage. So air quality of hospital environment, in restricted settings deserves attention, and requires long-term surveillance to protect both patients and healthcare workers.

The need for high-quality whole-genome sequence databases in microbial forensics.

PubMed

Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

2013-09-01

Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

Rural America's Stake in the Digital Economy. The Main Street Economist: Commentary on the Rural Economy.

ERIC Educational Resources Information Center

Staihr, Brian

This first article in a series on telecommunications in rural America provides an overview of several key telecommunication issues facing rural regions. High speed data services known as broadband have the potential to make rural areas less isolated and improve the rural quality of life, but physical barriers, sparse population density, and few…

Beginning to Understand Why New Hampshire's Rural Educators Chose Not to Join New Hampshire's Newly Developed On-Line Professional Learning Communities: A Quantitative and Qualitative Study

ERIC Educational Resources Information Center

Baker, Cheryl B.

2011-01-01

Rural educators face many barriers when trying to participate in high quality professional development, including isolation, funding issues, distance, and lack of temporary replacements. Technological solutions can assist rural educators in overcoming these barriers. Participating in on-line professional learning communities can provide New…

Mt. Graham red squirrel use of forest habitat: Historical, present, and future perspectives

Treesearch

Christopher D. O’Connor; John L. Koprowski; Ann M. Lynch; Donald A. Falk

2014-01-01

Geographically isolated populations of endangered species such as the Mount Graham red squirrel (MGRS) (Tamiasciurus hudsonicus grahamensis) are particularly sensitive to fluctuations in habitat quality and extent. In recent decades a series of insect outbreaks and high-severity fires degraded the sole MGRS habitat in the Pinaleño Mountains of southeast Arizona, and...

Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658

PubMed Central

Song, Ju Yeon; Yoo, Ran Hee; Jang, Song Yee; Seong, Won-Keun; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Park, Mi-Sun

2012-01-01

Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and animals. Here, we report the high-quality draft genome sequence of E. coli NCCP15658 isolated from a patient in the Republic of Korea. Its genome size was determined to be 5.46 Mb, and its genomic features, including genes encoding virulence factors, were analyzed. PMID:22740673

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE PAGES

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha; ...

2016-06-23

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

PubMed Central

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE. PMID:24688314

Study on design method and vibration reduction characteristic of floating raft with periodic structure

NASA Astrophysics Data System (ADS)

Fang, Yuanyuan; Zuo, Yanyan; Xia, Zhaowang

2018-03-01

The noise level is getting higher with the development of high-power marine power plant. Mechanical noise is one of the most obvious noise sources which not only affect equipment reliability, riding comfort and working environment, but also enlarge underwater noise. The periodic truss type device which is commonly applied in fields of aerospace and architectural is introduced to floating raft construction in ship. Four different raft frame structure are designed in the paper. The vibration transmissibility is taken as an evaluation index to measure vibration isolation effect. A design scheme with the best vibration isolation effect is found by numerical method. Plate type and the optimized periodic truss type raft frame structure are processed to experimental verify vibration isolation effect of the structure of the periodic raft. The experimental results demonstrate that the same quality of the periodic truss floating raft has better isolation effect than that of the plate type floating raft.

Rapid assessment of antimicrobial resistance prevalence using a Lot Quality Assurance sampling approach.

PubMed

van Leth, Frank; den Heijer, Casper; Beerepoot, Mariëlle; Stobberingh, Ellen; Geerlings, Suzanne; Schultsz, Constance

2017-04-01

Increasing antimicrobial resistance (AMR) requires rapid surveillance tools, such as Lot Quality Assurance Sampling (LQAS). LQAS classifies AMR as high or low based on set parameters. We compared classifications with the underlying true AMR prevalence using data on 1335 Escherichia coli isolates from surveys of community-acquired urinary tract infection in women, by assessing operating curves, sensitivity and specificity. Sensitivity and specificity of any set of LQAS parameters was above 99% and between 79 and 90%, respectively. Operating curves showed high concordance of the LQAS classification with true AMR prevalence estimates. LQAS-based AMR surveillance is a feasible approach that provides timely and locally relevant estimates, and the necessary information to formulate and evaluate guidelines for empirical treatment.

Preparation of RNA from bacteria infected with bacteriophages: a case study from the marine unicellular Synechococcus sp. WH7803 infected by phage S-PM2.

PubMed

Shan, Jinyu; Clokie, Martha

2009-01-01

Bacteriophages manipulate bacterial gene expression in order to express their own genes or influence bacterial metabolism. Gene expression can be studied using real-time PCR or microarrays. Either technique requires the prior isolation of high quality RNA uncontaminated by the presence of genomic DNA. We outline the considerations necessary when working with bacteriophage infected bacterial cells. We also give an example of a protocol for extraction and quantification of high quality RNA from infected bacterial cells, using the marine cyanobacterium WH7803 and the phage S-PM2 as a case study. This protocol can be modified to extract RNA from the host/bacteriophage of interest.

Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica sub...

An efficient, reliable and inexpensive device for the rapid homogenization of multiple tissue samples by centrifugation.

PubMed

Ilyin, S E; Plata-Salamán, C R

2000-02-15

Homogenization of tissue samples is a common first step in the majority of current protocols for RNA, DNA, and protein isolation. This report describes a simple device for centrifugation-mediated homogenization of tissue samples. The method presented is applicable to RNA, DNA, and protein isolation, and we show examples where high quality total cell RNA, DNA, and protein were obtained from brain and other tissue samples. The advantages of the approach presented include: (1) a significant reduction in time investment relative to hand-driven or individual motorized-driven pestle homogenization; (2) easy construction of the device from inexpensive parts available in any laboratory; (3) high replicability in the processing; and (4) the capacity for the parallel processing of multiple tissue samples, thus allowing higher efficiency, reliability, and standardization.

Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality

Treesearch

Kellie J. Carim; Lisa A. Eby; Craig A. Barfoot; Matthew C. Boyer

2016-01-01

Fragmentation and isolation of wildlife populations has reduced genetic diversity worldwide, leaving many populations vulnerable to inbreeding depression and local extinction. Nonetheless, isolation is protecting many native aquatic species from interactions with invasive species, often making reconnection an unrealistic conservation strategy. Isolation management is...

Marital Quality as a Moderator of the Effects of Poor Vision on Quality of Life Among Older Adults

PubMed Central

2011-01-01

Objectives. This study assessed the moderating role of marital quality in the effects of subjective and objective vision on functional limitations, social isolation, and depressive symptomatology. Method. Data from 738 married older adults drawn from a probability-based representative sample of elders residing in the United States were used. Assessments included subjective and objective vision, marital quality variables (relationship satisfaction, supportive spouse behaviors, and free time spent with one’s spouse), and three aspects of quality of life (functional limitations, social isolation, and depressive symptomatology). Results. Moderated regression analyses found that relationship satisfaction and supportive spouse behaviors moderated the effects of poor self-reported vision on functional limitations and depressive symptoms and the effects of poor visual acuity on functional limitations. As hypothesized, poorer vision was unrelated to functional limitations and depressive symptoms in more satisfying marriages but predicted higher levels of both outcomes in less satisfying marriages. Contrary to expectations, higher levels of supportive spouse behaviors were associated with more functional limitations in respondents who reported poorer subjective and objective vision. Discussion. A marriage that is highly satisfying can mitigate the adverse effects of poor vision on functional limitations and depressive symptomatology in late life. The moderating role of supportive spouse behaviors in the link between poor vision and quality of life is less intuitive, however. Whereas relationship satisfaction may operate as a traditional buffer in the context of poor vision, supportive spouse behaviors may increase in response to or be ineffective in this context. PMID:21840838

Short term effects on bone quality associated with consumption of soy protein isolate and other dietary protein sources in rapidly growing female rats

USDA-ARS?s Scientific Manuscript database

Beneficial effects of soy protein consumption on bone quality have been reported. The effects of other dietary protein sources such as whey protein hydrolysate (WPH) and rice protein isolate (RPI) on bone growth has been less well examined. The current study compared effects of feeding soy protein i...

Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring

PubMed Central

Kim, Byung Kwon; Lee, Seong Hyuk; Kim, Seon-Young; Jeong, Haeyoung; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su

2012-01-01

Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological research and biotechnological applications. Here we report the high-quality draft genome sequence of T. zilligii AN1T. The genome contains a number of genes for an immune system and adaptation to a microbial biomass-rich environment as well as hydrogenase genes. PMID:22740682

Genomes of Salmonella with diverse patterns of antibiotic resistance (AR) revealed the dynamics of AR gene organization and detected resistance gene families found in Salmonella

USDA-ARS?s Scientific Manuscript database

We produced and assembled high quality draft genomes (~100X coverage) for 305 Salmonella from a diverse a group of over 100 serovars and diverse sources. Of these isolates, 119 were selected to capture a wide variety of different AR patterns. In our subsequent analyses we included 285 additional pub...

High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China

DOE PAGES

Mefferd, Chrisabelle C.; Zhou, En-Min; Yu, Tian-Tian; ...

2016-04-28

The draft genomes ofThermus  tengchongensisYIM 77401 andT. caliditerraeYIM 77777 are 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes, respectively. Gene content and growth experiments demonstrate broad metabolic capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation, incomplete denitrification, and polysulfide reduction.

High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1 T Isolated from Great Boiling Spring, Nevada

DOE PAGES

Ganji, Rakesh; Murugapiran, Senthil K.; Ong, John C.; ...

2016-10-20

The draft genome of Thermocrinis jamiesonii GBS1 T is 1,315,625 bp in 10 contigs and encodes 1,463 predicted genes. The presence of sox genes and various glycoside hydrolases and the absence of uptake NiFe hydrogenases ( hyaB) are consistent with a requirement for thiosulfate and suggest the ability to use carbohydrate polymers.

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling

PubMed Central

Schreck, Katharina; Herbold, Craig W.; Daims, Holger; Wagner, Michael; Loy, Alexander

2018-01-01

ABSTRACT The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation. PMID:29371357

Social Disruption and Psychological Stress in an Alaskan Fishing Community: The Impact of the Exxon Valdez Oil Spill.

ERIC Educational Resources Information Center

Picou, J. Steven; And Others

Technological accidents such as the Exxon Valdez oil spill in 1989 create man-made disaster situations that threaten community survival and the well-being and quality of life of community residents. This paper focuses on the social and psychological impact of the 1989 oil spill on Cordova, an isolated Alaskan community with high economic…

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi.

PubMed

Solomon, Kevin V; Henske, John K; Theodorou, Michael K; O'Malley, Michelle A

2016-04-01

Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80 °C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Antimicrobial-Resistance Genetic Markers in Potentially Pathogenic Gram Positive Cocci Isolated from Brazilian Soft Cheese.

PubMed

Resende, Juliana Alves; Fontes, Cláudia Oliveira; Ferreira-Machado, Alessandra Barbosa; Nascimento, Thiago César; Silva, Vânia Lúcia; Diniz, Cláudio Galuppo

2018-02-01

Although most Brazilian dairy products meet high technological standards, there are quality issues regarding milk production, which may reduce the final product quality. Several microbial species may contaminate milk during manufacture and handling. If antimicrobial usage remains uncontrolled in dairy cattle, the horizontal transfer of antimicrobial resistance genes in foodstuffs may be of particular concern for both food producers and dairy industry. This study focused on the evaluation of putative Gram positive cocci in Minas cheese and of antimicrobial and biocide resistance genes among the isolated bacteria. Representative samples of 7 different industrially trademarked Minas cheeses (n = 35) were processed for selective culture and isolation of Gram positive cocci. All isolated bacteria were identified by DNA sequencing of the 16S rRNA gene. Antimicrobial resistance genes were screened by PCR. Overall, 208 strains were isolated and identified as follows: Enterococcus faecalis (47.6%), Macrococcus caseolyticus (18.3%), Enterococcus faecium (11.5%), Enterococcus caseliflavus (7.7%), Staphylococcus haemolyticus (7.2%), Staphylococcus aureus (4.3%), Staphylococcus epidermidis (2.9%), and Enterococcus hirae (0.5%). The genetic markers mecA (78.0%) and smr (71.4%) were the most prevalent, but others were also detected, such as blaZ (65.2%), msrA (60.9%), msrB (46.6%), linA (54.7%), and aacA-aphD (47.6%). The occurrence of opportunist pathogenic bacteria harboring antimicrobial resistance markers in the cheese samples are of special concern, since these bacteria are not considered harmful contaminating agents according to the Brazilian sanitary regulations. However, they are potentially pathogenic bacteria and the cheese may be considered a reservoir for antimicrobial resistance genes available for horizontal transfer through the food chain, manufacturing personnel and consumers. © 2018 Institute of Food Technologists®.

Model photoautrophs isolated from a Proterozoic ocean analog - aerobic life under anoxic conditions

NASA Astrophysics Data System (ADS)

Hamilton, T. L.; de Beer, D.; Klatt, J.; Macalady, J.; Weber, M.; Lott, C.; Chennu, A.

2016-12-01

The 1-2 billion year delay before the final rise of oxygen at the end of the Proterozoic represents an important gap in our understanding of ancient biogeochemical cycling. Primary production fueled by sulfide-dependent anoxygenic photosynthesis, including the activity of metabolically versatile cyanobacteria, has been invoked as a mechanism for sustaining low atmospheric O2 throughout much of the Proterozoic. However, we understand very little about photoautotrophs that inhabit Proterozoic-like environments present on Earth today. Here we report on the isolation and characterization of a cyanobacterium and a green sulfur bacterium that are the dominant members of pinnacle mats in Little Salt Spring—a karst sinkhole in Florida with perennially low levels of dissolved oxygen and sulfide. The red pinnacle mats bloom in the anoxic basin of the sinkhole and receive light that is of very poor quality to support photosynthesis. Characterization of the isolates is consistent with observations of oxygenic and anoxygenic photosynthesis in situ—both organisms perform anoxygenic photosynthesis under conditions of very low light quality and quantity. Oxygenic photosynthesis by the cyanobacterium isolate is inhibited by the presence of sulfide and under optimal light conditions, rates of anoxygenic photosynthesis are nearly double that of oxygenic photosynthesis. The green sulfur bacterium is tolerant of oxygen and has a very low affinity for sulfide. In Little Salt Spring, oxygenic photosynthesis occurs for only four hours a day and the water column remains anoxic because of a continuous supply of sulfide. Isolation and characterization of these photoautotrophs combined with our high resolution microsensor data in situ highlight microbial biogeochemical cycling in this exceptional site where aerobic microorganisms persist in a largely anoxic ecosystem.

Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population.

PubMed

Clark, Clifford G; Berry, Chrystal; Walker, Matthew; Petkau, Aaron; Barker, Dillon O R; Guan, Cai; Reimer, Aleisha; Taboada, Eduardo N

2016-12-03

Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates. Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain. The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.

Performance of ELISA antigens prepared from 8 isolates of porcine reproductive and respiratory syndrome virus with homologous and heterologous antisera.

PubMed Central

Cho, H J; Entz, S C; Magar, R; Joo, H S

1997-01-01

Porcine reproductive and respiratory syndrome virus (PRRSV) ELISA antigens of high quality were produced using 8 different isolates of PRRSV: the European Lelystad virus (LV), the U.S. MN-1b, 89-46448, 93-44927, and 93-24025B, and the Canadian LHVA-93-3, PA-8 and GH-6 virus isolates. The performance of each of these 8 antigens and a commercial PRRSV antibody test kit (Idexx's HerdChek) were measured against antisera raised in 5 groups of 6 piglets inoculated with either LV, MN-1b, 89-46448, 93-44927, or 93-24025B. Among the 8 isolates, the 89-46448 isolate produced the broadest spectrum of antigen and resulted in earlier detection of antibodies to various North American PRRSV isolates, followed by MN-1b as the 2nd best ELISA antigen for the detection of North American PRRSV antibodies. The GH-6 and PA-8 viral antigens exhibited restricted detection of PRRSV antibodies. The LV and 89-46448 combined antigens produced the best performance for the detection of antibodies against both European and North American antigenic types of PRRSV. Using 173 panel samples collected at 11 to 60 d after intranasal inoculation with 1 of the 5 PRRSV isolates, the sensitivities of the indirect ELISA used were 73.4%, 98.3%, 90.8%, 98.3%, 83.2%, 93.1%, 77.1%, 64.2%, 98.8% and 95.9% for LV, MN-1b, LHVA-93-3, 89-46448, 93-44927, 93-24025B, PA-8, GH-6 antigens, 89-46448-LV combined antigens and Idexx's PRRSV antibody test kit, respectively. All 8 antigens gave negative results with preinfection porcine sera (n = 30); high background or nonspecific reactions were not observed with the antigens. PMID:9342455

Isolation of GMP Grade Human Hepatocytes from Remnant Liver Tissue of Living Donor Liver Transplantation.

PubMed

Enosawa, Shin

2017-01-01

For the purpose of clinical research of hepatocyte transplantation, procedures for isolation, cryopreservation, thawing, and functional assessment of hepatocytes are described. Although demands for human hepatocytes are increasing in not only cell therapy but also drug development, it is highly difficult to obtain good lots of hepatocytes from human liver tissue. This chapter describes essential issues such as alleviation of warm ischemia, prevention of shear stress, optimization of cryopreservation, and functional assessment, along with securement of quality. All procedures described here are compliant with good manufacturing procedure (GMP) in cell processing facility, approved by the act on measures to ensure safety of regenerative medicine and ethical regulations in Japan.

Structural assignment of poecillastrins B and C, macrolide lactams from the deep-water Caribbean sponge Poecillastra species.

PubMed

Takada, Kentaro; Choi, Byoung W; Rashid, Mohammad A; Gamble, William R; Cardellina, John H; Van, Que N; Lloyd, John R; McMahon, James B; Gustafson, Kirk R

2007-03-01

Two new chondropsin-type macrolide lactams, poecillastrins B (1) and C (2), were isolated from aqueous extracts of the marine sponge Poecillastra sp. These trace metabolites were isolated in low yield (400-600 microg), and their structures were determined primarily by analysis of NMR data acquired using a cyrogenically cooled probe. High-quality 1D and 2D NMR data sets allowed complete assignment of the spectroscopic data and defined the new structures as 35-membered ring analogues of poecillastrin A (3). Compounds 1 and 2 showed potent cytotoxic activity against a human melanoma tumor cell line (LOX) with an IC50 value of less than 1 microg/mL.

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Louie, Tiffany S.; Giovannelli, Donato; Yee, Nathan

Sedimenticola selenatireducens strain AK4OH1 T (= DSM 17993 T = ATCC BAA-1233 T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1 T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. Furthermore, the draft genome comprises 4,588,530 bpmore » and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. We report the main features of the genome of S. selenatireducens strain AK4OH1 T.« less

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

DOE PAGES

Louie, Tiffany S.; Giovannelli, Donato; Yee, Nathan; ...

2016-09-08

Sedimenticola selenatireducens strain AK4OH1 T (= DSM 17993 T = ATCC BAA-1233 T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1 T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. Furthermore, the draft genome comprises 4,588,530 bpmore » and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. We report the main features of the genome of S. selenatireducens strain AK4OH1 T.« less

Inattentional blindness and the von Restorff effect.

PubMed

Schmidt, Stephen R; Schmidt, Constance R

2015-02-01

Sometimes we fail to notice distinctive or unusual items (inattentional blindness), while other times we remember distinctive items more than expected items (the von Restorff effect). A three-factor framework is presented and tested in two experiments in an attempt to reconcile these seemingly contradictory phenomena. Memory for different types of unexpected stimuli was tested after an easy or difficult Stroop color-naming task. Highly arousing taboo words were well remembered even when the difficult Stroop task limited attentional resources. However, a conceptual isolation effect was only observed when the nature of the category change was highlighted by the Stroop task, the Stroop task was easy, and/or the isolated targets enjoyed a retrieval advantage relative to comparison targets. As proposed in the three-factor framework, the arousing qualities of the stimuli, the attentional demands of the primary task, and the relevance of isolated features at encoding and retrieval combine to produce inattentional blindness and the von Restorff effect.

Perceived stigmatization and its impact on quality of life - results from a large register-based study including breast, colon, prostate and lung cancer patients.

PubMed

Ernst, J; Mehnert, A; Dietz, A; Hornemann, B; Esser, P

2017-11-09

To date, research on stigmatization among cancer patients and related psychosocial consequences has been scarce and mostly based on small and highly selected samples. We investigated stigmatization and its impact on quality of life among a large sample including four major tumor entities. We assessed 858 patients with breast, colon, lung or prostate cancer from two cancer registries. Stigmatization and quality of life (QoL) was assessed with the Social Impact Scale (SIS-D) and the EORTC Quality of Life Questionnaire (European Organization for Research and Treatment of Cancer), respectively. Group effects were analyzed via analyses of variance, relationships were investigated via Pearson's r and stepwise regression analyses. The mean age was 60.7 years, 54% were male. Across cancer sites, the dimensions of stigmatization (isolation, social rejection, financial insecurity and internalized shame) were in the lower and middle range, with the highest values found for isolation. Stigmatization was lowest among prostate cancer patients. Stigmatization predicted all five areas of QoL among breast cancer patients (p < .05), but only affected emotional functioning (p < .01) among lung cancer patients. We found an inverse relationship between perceived cancer-related stigmatization and various dimensions of QoL, with variation between cancer sites. Breast cancer patients should be focused in individual therapies regarding the negative consequences accompanied by perceived stigmatization.

Effect of whey protein isolate-pullulan edible coatings on the quality and shelf life of freshly roasted and freeze-dried Chinese chestnut.

PubMed

Gounga, M E; Xu, S-Y; Wang, Z; Yang, W G

2008-05-01

Harvested chestnut is characterized by a short shelf life, exposing many Chinese producers to a storage problem as product losses are very high. The objective of this study was to develop a suitable technology to extend the shelf life of harvested chestnut fruits for commercial use. The effect of whey protein isolate-pullulan (WPI-Pul) coating on fresh-roasted chestnuts (FRC) and roasted freeze-dried chestnut (RFDC) quality and shelf life was studied under 2 different storage temperature (4 and 20 degrees C) conditions. Coatings were formed directly onto the surface of the fruits by dipping them into a film solution. SEM micrographs showed homogeneous WPI-Pul to cover the whole surface of chestnut with good adherence and perfect integrity. Moisture loss or gain, fruit quality, and shelf life were evaluated by weight loss or gain, surface color development, and visible decay during the storage period of 15 to 120 d at 4 and 20 degrees C, respectively. WPI-Pul coating had a low, yet significant effect on reducing moisture loss and decay incidence of FRC, hence delaying changes in their external color. The results were satisfactory when the coating was done with freeze-drying at low temperature storage, thus improving the quality and increasing the shelf life. This provides an alternative strategy to minimize the significant losses in harvested chestnut.

Performance Analysis of Isolated Hybrid Power Plant Model with Dynamic Load Conditions - Morning, Noon and Afternoon Transitions

NASA Astrophysics Data System (ADS)

Irawati, Rina

2018-02-01

Diesel Generator with Photovoltaic Hybrid Power Plant is one of the solutions for supply electric demand to isolated area. The energy sources that can be used for hybrid system are such as photovoltaic, wind turbine, and biomass or biogas, because these sources are almost available in every isolated area. This research used a model of hybrid system from diesel generator and 1.28 kWp photovoltaic power plant. The reliability and some of power quality of this system tested by 1300VA house hold daily load characteristic effectively 24 hour. Power quality and some electricity parameters during transition mode for each resource will be analyzed. Furthermore the power quality analyze will be conducted and evaluated base on Electrical Engineers' Association (EEA).

Reconnaissance of Surface-Water Quality and Possible Sources of Nutrients and Bacteria in the Turkey Creek Watershed, Northwest Oklahoma, 2002-2003

USGS Publications Warehouse

Becker, Carol J.

2004-01-01

The U.S. Geological Survey in cooperation with the Oklahoma Department of Environmental Quality and the U.S. Environmental Protection Agency investigated the distribution of surface-water quality and possible sources of nutrients and Escherichia coli bacteria to surface water in Turkey Creek, which flows about 70 miles through mostly rural agricultural areas in northwest Oklahoma. Results show that discharge on the main stem of Turkey Creek increased during low-flow conditions from an average of 5.4 cubic feet per second at the upper most site to 39 cubic feet per second at the lower most site in the watershed, indicating that Turkey Creek gains water from ground-water discharge. A portion of the increase in stream discharge may be from discharges of treated effluent from city sewage lagoons. However, the volume and frequency of discharges are unknown. Surface-water-quality samples show that specific conductance ranged from 1,180 to 1,740 microsiemens per centimeter at 25 degrees Celsius during low-flow conditions and in general, decreased downstream with site 1 or site 2 having the largest measurement and site 5 having the lowest. The pH values were slightly alkaline and ranged from 6.8 to 8.5 with a median of 8.2. Dissolved oxygen ranged from 9.3 to 15.9 milligrams per liter in samples collected in the months of November, February, and March and ranged from 5.3 to 13.9 milligrams per liter in samples collected in the months of June, July, and August. Surface-water-quality samples show that the median concentrations of nitrite plus nitrate as nitrogen (1.16 milligrams per liter) and total phosphorus (0.275 milligram per liter) are larger than the average median concentrations of 0.35 and 0.083 milligram per liter, respectively, calculated from water-quality sites in Oklahoma and part of Arkansas (excluding sites in the Ozark Highland and the Ouachita Mountains ecoregions) having similar stream orders and stream slopes. Concentrations of nitrite plus nitrate as nitrogen increased slightly in the winter months and decreased in the summer months, whereas, concentrations of total phosphorus and orthophosphate as phosphorus tended to increase during the summer months and decrease in the winter months. During high-flow conditions total phosphorus increased 7.7 times above the average concentration of 0.261 milligram per liter in low-flow samples. Orthophosphate concentrations increased 3.5 to 4 times during high-flow conditions. Almost all low-flow samples showed 15N values between 4 and 10 parts per thousand, above the range for atmospheric nitrogen and synthetic fertilizer and below the range for animal waste. These samples may represent a mixture of nitrate from these two sources and other sources enriched with 15N, such as soils and plants. Results of the bacterial source tracking indicated that the two source groups having the greatest number of ribopattern matches with surface-water isolates were the cattle group, 53 isolates or 23.5 percent, and the human group, 41 isolates or 18.2 percent. Fewer surface-water isolates matched the deer and horse groups, 8.0 percent and 3.5 percent, respectively. About 43 percent or 96 surface-water isolates were not matched to any source group.

Clonally Related Neisseria gonorrhoeae Isolates with Decreased Susceptibility to the Extended-Spectrum Cephalosporin Cefotaxime in Amsterdam, the Netherlands

PubMed Central

Heymans, Raymond; Bruisten, Sylvia M.; Golparian, Daniel; Unemo, Magnus; de Vries, Henry J. C.

2012-01-01

From 2006 to 2008, Neisseria gonorrhoeae isolates were identified with decreased susceptibility to the extended-spectrum cephalosporin (ESC) cefotaxime among visitors of the Amsterdam sexually transmitted infections (STI) clinic, the Netherlands. Spread, clonality, and characteristics of 202 isolates were examined using antibiograms, conventional penA mosaic gene PCR, and N. gonorrhoeae multiple-locus variable-number tandem repeat analysis (NG-MLVA). A strictly defined subset was further characterized by N. gonorrhoeae multiantigen sequence typing (NG-MAST) and sequencing of ESC resistance determinants (penA, mtrR, and porB1b). Seventy-four N. gonorrhoeae isolates with a cefotaxime MIC of >0.125 μg/ml (group A), 54 with a cefotaxime MIC of 0.125 μg/ml (group B), and a control group of 74 with a cefotaxime MIC of <0.125 μg/ml (group C) were included. Fifty-three clonally related penA mosaic-positive isolates (penicillin-binding protein 2 type XXXIV) were identified in group A (n = 47 isolates; 64%) and B (n = 6 isolates; 11%). The 53 penA mosaic-positive isolates were predominantly NG-MAST ST1407 (87%) and contained an mtrR promoter A deletion (98%) and porB1b alterations G101K/A102N. All were assigned to the same NG-MLVA cluster that comprised in total 56 isolates. A correlation was found between decreased cefotaxime susceptibility and ST1407 that was highly prevalent among visitors of the Amsterdam STI clinic. The rapid spread of this strain, which also has been identified in many other countries, might be facilitated by high-risk sexual behavior and should be monitored closely to identify potential treatment failure. Quality-assured surveillance of ESC susceptibility on the national and international levels and exploration of new drugs and/or strategies for treatment of gonorrhea are crucial. PMID:22214779

Social support network, mental health and quality of life: a cross-sectional study in primary care.

PubMed

Portugal, Flávia Batista; Campos, Mônica Rodrigues; Correia, Celina Ragoni; Gonçalves, Daniel Almeida; Ballester, Dinarte; Tófoli, Luis Fernando; Mari, Jair de Jesus; Gask, Linda; Dowrick, Christopher; Bower, Peter; Fortes, Sandra

2016-12-22

The objective of this study was to identify the association between emotional distress and social support networks with quality of life in primary care patients. This was a cross-sectional study involving 1,466 patients in the cities of São Paulo and Rio de Janeiro, Brazil, in 2009/2010. The General Health Questionnaire, the Hospital Anxiety and Depression Scale and the brief version of the World Health Organization Quality of Life Instrument were used. The Social Support Network Index classified patients with the highest and lowest index as socially integrated or isolated. A bivariate analysis and four multiple linear regressions were conducted for each quality of life outcome. The means scores for the physical, psychological, social relations, and environment domains were, respectively, 64.7; 64.2; 68.5 and 49.1. In the multivariate analysis, the psychological domain was negatively associated with isolation, whereas the social relations and environment domains were positively associated with integration. Integration and isolation proved to be important factors for those in emotional distress as they minimize or maximize negative effects on quality of life.

An optimized method for high quality DNA extraction from microalga Prototheca wickerhamii for genome sequencing.

PubMed

Jagielski, Tomasz; Gawor, Jan; Bakuła, Zofia; Zuchniewicz, Karolina; Żak, Iwona; Gromadka, Robert

2017-01-01

The complex cell wall structure of algae often precludes efficient extraction of their genetic material. The purpose of this study was to design a next-generation sequencing-suitable DNA isolation method for unicellular, achlorophyllous, yeast-like microalgae of the genus Prototheca , the only known plant pathogens of both humans and animals. The effectiveness of the newly proposed scheme was compared with five other, previously described methods, commonly used for DNA isolation from plants and/or yeasts, available either as laboratory-developed, in-house assays, based on liquid nitrogen grinding or different enzymatic digestion, or as commercially manufactured kits. All five, previously described, isolation assays yielded DNA concentrations lower than those obtained with the new method, averaging 16.15 ± 25.39 vs 74.2 ± 0.56 ng/µL, respectively. The new method was also superior in terms of DNA purity, as measured by A260/A280 (-0.41 ± 4.26 vs 2.02 ± 0.03), and A260/A230 (1.20 ± 1.12 vs 1.97 ± 0.07) ratios. Only the liquid nitrogen-based method yielded DNA of comparable quantity (60.96 ± 0.16 ng/µL) and quality (A260/A280 = 2.08 ± 0.02; A260/A230 = 2.23 ± 0.26). Still, the new method showed higher integrity, which was best illustrated upon electrophoretic analysis. Genomic DNA of Prototheca wickerhamii POL-1 strain isolated with the protocol herein proposed was successfully sequenced on the Illumina MiSeq platform. A new method for DNA isolation from Prototheca algae is described. The method, whose protocol involves glass beads pulverization and cesium chloride (CsCl) density gradient centrifugation, was demonstrated superior over the other common assays in terms of DNA quantity and quality. The method is also the first to offer the possibility of preparation of DNA template suitable for whole genome sequencing of Prototheca spp.

Microbiological Quality of Raw Dried Pasta from the German Market, with Special Emphasis on Cronobacter Species.

PubMed

Akineden, Ömer; Murata, Kristina Johanna; Gross, Madeleine; Usleber, Ewald

2015-12-01

The microbiological quality of 132 dried pasta products available on the German market, originating from 11 different countries, was studied. Sample materials included soft or durum wheat products, some of which produced with other ingredients such as eggs, spices, or vegetables. Parameters included hygiene indicators (aerobic plate count, mold count, the presence of Enterobacteriaceae) and pathogenic/toxinogenic bacterial species (Salmonella spp., Staphylococcus aureus, presumptive Bacillus cereus, and Cronobacter spp.). The overall results of hygiene parameters indicated a satisfactory quality. Salmonella was not found in any sample. Three samples were positive for S. aureus (10(2) to 10(4) colony forming unit (CFU)/g). Presumptive B. cereus at levels of 10(3) to 10(4) CFU/g were detected in 3 samples. Cronobacter spp. were isolated from 14 (10.6%) products. Of these, 9 isolates were identified as C. sakazakii, 2 each as C. turicensis and C. malonaticus, and 1 as C. muytjensii. The isolates were assigned to 9 multilocus sequence typing (MLST) sequence types and to 14 different PFGE profiles. Although pasta products are typically cooked before consumption, some consumers, and children in particular, may also eat raw pasta as nibbles. Raw pasta seems to be a relevant source of exposure to dietary Cronobacter spp., although health risks are probably restricted to vulnerable consumers. High numbers of presumptive B. cereus as found in some samples may be a risk after improper storage of cooked pasta products because toxinogenic strains are frequently found within this species. © 2015 Institute of Food Technologists®

Switchable and tunable film bulk acoustic resonator fabricated using barium strontium titanate active layer and Ta{sub 2}O{sub 5}/SiO{sub 2} acoustic reflector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sbrockey, N. M., E-mail: sbrockey@structuredmaterials.com; Tompa, G. S.; Kalkur, T. S.

2016-08-01

A solidly mounted acoustic resonator was fabricated using a Ba{sub 0.60}Sr{sub 0.40}TiO{sub 3} (BST) film deposited by metal organic chemical vapor deposition. The device was acoustically isolated from the substrate using a Bragg reflector consisting of three pairs of Ta{sub 2}O{sub 5}/SiO{sub 2} layers deposited by chemical solution deposition. Transmission electron microscopy verified that the Bragg reflector was not affected by the high temperatures and oxidizing conditions necessary to process high quality BST films. Electrical characterization of the resonator demonstrated a quality factor (Q) of 320 and an electromechanical coupling coefficient (K{sub t}{sup 2}) of 7.0% at 11 V.

Comparison of Plasma Exosomes by Differential Ultracentrifugation and Solvent Precipitation Methods.

PubMed

Peng, Qiao; Zhang, Jing; Zhou, Gang

2018-06-01

Emerging evidence has identified that exosomes play a pivotal role in intercellular signal transmission. However, the standardized purification techniques to isolate high quality exosomes are still deficient at present. This study was to evaluate reproducibility and efficiency of differential ultracentrifugation and solvent precipitation-based kits by isolating plasma-derived exosomes from oral lichen planus patients. Morphology, exosomal biomarkers, particle size distribution, proteomic components, and protein yield of isolated exosomes were evaluated by transmission electron microscope, western blot, laser diffraction instrument, Coomassie staining, and BCA protein assay kit, respectively. TEM displayed representative cup-shaped morphology of exosomes and western blot identified exosomal biomarkers CD9 and CD63. The size distribution showed that particles by differential ultracentrifugation were mainly from 26.15 nm to 166.5 nm, while some of the particles obtained by solvent precipitation kits were larger than 1,000 nm. In addition, exosomes isolated by solvent precipitation kits showed a significantly higher amount of protein yield due to plasma albumin contamination. Both differential ultracentrifugation and precipitation based kits could successfully isolate plasma exosomes, and exosomes by differential ultracentrifugation were purer and more appropriate for further proteomic analysis.

Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils.

PubMed

Mahmoudi, Nagissa; Slater, Greg F; Fulthorpe, Roberta R

2011-08-01

Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid-liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.

Airborne microorganisms cultivable on naturally ventilated document repositories of the National Archive of Cuba.

PubMed

Borrego, Sofía; Perdomo, Ivette

2016-02-01

The quality of the indoor air can provide very useful information for the artwork conservation. The aim of the study was to evaluate the microbial concentration inside six document repositories of the National Archive of the Republic of Cuba in two months of 1 year. The repositories are large, high, and have a natural cross-ventilation system. The microbial sampling was done in July 2010 (summer or rainy month) and February 2011 (winter or dry month) using the SAS Super 100 biocollector at 100 L/min. An appropriate selective culture media were used to isolate fungi and bacteria. A high total microbial concentration on the north side of the building in two studied months was observed. The fungal concentrations were significantly higher in July 2010 in all repositories, while the bacterial concentrations were significantly higher mostly in February 2011 only in repositories located on the first and second floor of the building. Eight fungal genera in the indoor air of all environments were isolated. Regardless of the side of the analyzed building, Penicillium, Aspergillus, and Cladosporium were the predominant genera. Aspergillus flavus and Aspergillus niger were the species isolated in almost all of the analyzed repositories in the studied months. Gram-positive bacteria prevailed among bacterial groups isolated from indoor air repositories, and some percentages corresponded to the genera Bacillus and Streptomyces. In Cuba, the temperature and relative humidity are high during the whole year but the natural ventilation plays an important role in retarding microbial growth on materials.

Fabrication and transport property of artificial structure of CNTs using SPM nano-manipulation

NASA Astrophysics Data System (ADS)

Maejima, K.; Kida, M.; Yaguchi, Y.; Sudo, K.; Kawamura, T.; Morimoto, T.; Aoki, N.; Ochiai, Y.

2007-04-01

We have established a novel manipulation technique using a glass-micro capillary under a high-resolution CCD microscope so far. Two isolated multi-wall carbon nanotubes (MWNTs) are settled to form a well-aligned cross structure. Recently, we have tried to develop a fine manipulation system using a scanning probe microscope with a silicon cantilever. Therefore, thinner high-quality MWNTs (˜10 nm in diameter) can be utilized in this system. At the junction, we have observed weak localization and Fano-like-effect, zero bias anomaly whose traces were visible even at room temperature with thick MWNTs (˜100 nm in diameter). On the other hand, with thinner high-quality MWNTs (˜10 nm in diameter), we have observed also anomalous I-V characteristic and Altshuler-Aronov-Spivak-like magneto-oscillations at low temperature in the nano-space transport.

Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei).

PubMed

Xia, Chongjing; Wang, Meinan; Yin, Chuntao; Cornejo, Omar E; Hulbert, Scot; Chen, Xianming

2018-05-24

Puccinia striiformis f. sp. tritici (Pst) causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei (Psh) causes stripe rust on barley. Several Pst genomes are available, but no Psh genome is available. More genomes of Pst and Psh are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced Pst isolate 93-210 and Psh isolate 93TX-2 using PacBio and Illumina technologies, and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interaction.

Design and development of a prototype platform for gait analysis

NASA Astrophysics Data System (ADS)

Diffenbaugh, T. E.; Marti, M. A.; Jagani, J.; Garcia, V.; Iliff, G. J.; Phoenix, A.; Woolard, A. G.; Malladi, V. V. N. S.; Bales, D. B.; Tarazaga, P. A.

2017-04-01

The field of event classification and localization in building environments using accelerometers has grown significantly due to its implications for energy, security, and emergency protocols. Virginia Tech's Goodwin Hall (VT-GH) provides a robust testbed for such work, but a reduced scale testbed could provide significant benefits by allowing algorithm development to occur in a simplified environment. Environments such as VT-GH have high human traffic that contributes external noise disrupting test signals. This paper presents a design solution through the development of an isolated platform for data collection, portable demonstrations, and the development of localization and classification algorithms. The platform's success was quantified by the resulting transmissibility of external excitation sources, demonstrating the capabilities of the platform to isolate external disturbances while preserving gait information. This platform demonstrates the collection of high-quality gait information in otherwise noisy environments for data collection or demonstration purposes.

Interpretation of Borehole Geophysical Logs, Aquifer-Isolation Tests, and Water-Quality Data for Sites 1, 3, and 5 at the Willow Grove Naval Air Station/Joint Reserve Base, Horsham Township, Montgomery County, Pennsylvania: 2005

USGS Publications Warehouse

Sloto, Ronald A.

2007-01-01

Borehole geophysical logging, heatpulse-flowmeter measurements, borehole television surveys, and aquifer-isolation tests were conducted in 2005 at the Willow Grove Naval Air Station/Joint Reserve Base (NAS/JRB) in Horsham Township, Montgomery County, Pa. This study was done by the U.S. Geological Survey (USGS) in cooperation with the U.S. Navy in support of hydrogeological investigations to address ground-water contamination. Data collected for this study are valuable for understanding ground-water flow in the Stockton Formation at the local and regional scale. The Willow Grove NAS/JRB is underlain by the Stockton Formation, which consists of sedimentary rocks of Triassic age. The rocks of the Stockton Formation form a complex, heterogeneous aquifer with partially connected zones of high permeability. Borehole geophysical logs, heatpulse-flowmeter measurements, and borehole television surveys made in seven boreholes ranging from 70 to 350 ft deep were used to identify potential water-producing fractures and fracture zones and to select intervals for aquifer-isolation tests. An upward vertical hydraulic gradient was measured in one borehole, a downward vertical hydraulic gradient was measured in four boreholes, both an upward and a downward vertical hydraulic gradient were measured in one borehole, and no flow was measurable in one borehole. The aquifer-isolation tests isolated 30 discrete fractures in the seven boreholes for collection of depth-discrete hydraulic and water-quality data. Of the 30 fractures identified as potentially water producing, 26 fractures (87 percent) produced more than 1 gallon per minute of water. The specific capacity of the isolated intervals producing more than 1 gallon per minute ranged from 0.02 to 5.2 gallons per minute per foot. There was no relation between specific capacity and depth of the fracture. Samples for analysis for volatile organic compounds were collected from each isolated zone. Tetrachloroethylene (PCE) was the most prevalent compound at Site 1; concentrations were as great as 62 ?g/L (micrograms per liter). 1,1-dichloroethane was the most prevalent compound at Site 3; concentrations were as great as 9.3 ?g/L. Toluene was the most prevalent compound at Site 5; concentrations were as great as 77 ?g/L. For five out of the six wells (83 percent) sampled for field determinations of water-quality constituents, the interval with the lowest dissolved oxygen concentration had the highest total VOC concentration.

Vapor Phase Hydrogen Peroxide Sanitization of an Isolator for Aseptic Filling of Monoclonal Antibody Drug Product - Hydrogen Peroxide Uptake and Impact on Protein Quality.

PubMed

Hubbard, Aaron; Reodl, Thomas; Hui, Ada; Knueppel, Stephanie; Eppler, Kirk; Lehnert, Siegfried; Maa, Yuh-Fun

2018-03-15

A monoclonal antibody drug product (DP) manufacturing process was transferred to a different production site, where aseptic filling took place within an isolator that was sanitized using vapor phase hydrogen peroxide (VPHP). A quality-by-design approach was applied for study design to understand the impact of VPHP uptake in the isolator on DP quality. A combination of small-scale and manufacturing-scale studies was performed to evaluate the sensitivity of the monoclonal antibody to hydrogen peroxide (H2O2) as well as VPHP uptake mechanisms during the filling process. The acceptable H2O2 level was determined to be 100 ng/mL for the antibody in the H2O2 spiking study; protein oxidation was observed above this threshold. The most prominent sources of VPHP uptake were identified to be via the silicone tubing assembly (associated with the peristaltic pumps) and open, filled vials. Silicone tubing, an effective depot to H2O2, could absorb VPHP during different stages of the filling process and discharge H2O2 into the DP solution during filling interruptions. A small-scale isolator model, established to simulate manufacturing-scale conditions, was a useful tool in understanding H2O2 uptake in relation to tubing dimensions and VPHP concentration in the isolator air (or atmosphere). Although the tubing assembly had absorbed a substantial amount of VPHP during the decontamination phase, the majority of H2O2 could be removed during tubing cleaning and sterilization in the subsequent isolator aeration phase, demonstrating that H2O2 in the DP solution is taken up primarily via atmospheric VPHP residues in the isolator during filling. Picarro sensor monitoring suggested that the validated VPHP aeration process generates reproducible residual VPHP profiles in isolator air, thus allowing small-scale studies to provide more relevant recommendations on tubing size and interruption time limits for commercial manufacturing. The recommended process parameters were demonstrated to be acceptable and rendered no product quality impact as demonstrated in six consecutive manufacturing batches in the process validation campaign. Overall, this case study would provide process development scientists/engineers an in-depth understanding of the VPHP process and a science-based approach to mitigating DP quality impact. Copyright © 2018, Parenteral Drug Association.

High-quality forage production under salinity by using a salt-tolerant AtNXH1-expressing transgenic alfalfa combined with a natural stress-resistant nitrogen-fixing bacterium.

PubMed

Stritzler, Margarita; Elba, Pagano; Berini, Carolina; Gomez, Cristina; Ayub, Nicolás; Soto, Gabriela

2018-06-20

Alfalfa, usually known as the "Queen of Forages", is the main source of vegetable protein to meat and milk production systems worldwide. This legume is extremely rich in proteins due to its highly efficient symbiotic association with nitrogen-fixing strains. In the last years, alfalfa culture has been displaced to saline environments by other important crops, including major cereals, a fact that has reduced its biomass production and symbiotic nitrogen fixation. In this short communication, we report the high forage production and nutrient quality of alfalfa under saline conditions by alfalfa transformation with the AtNHX1 Na + /H + antiporter and inoculation with the stress-resistant nitrogen-fixing strain Sinorhizobium meliloti B401. Therefore, the incorporation of transgenic traits into salt-sensitive legumes in association with the inoculation with natural stress-resistant isolates could be a robust approach to improve the productivity and quality of these important nitrogen-fixing crops. Copyright © 2018. Published by Elsevier B.V.

Comparison of PV signal quality using a novel circular mapping and ablation catheter versus a standard circular mapping catheter.

PubMed

von Bary, Christian; Fredersdorf-Hahn, Sabine; Heinicke, Norbert; Jungbauer, Carsten; Schmid, Peter; Riegger, Günter A; Weber, Stefan

2011-08-01

Recently, new catheter technologies have been developed for atrial fibrillation (AF) ablation. We investigate the diagnostic accuracy of a circular mapping and pulmonary vein ablation catheter (PVAC) compared with a standard circular mapping catheter (Orbiter) and the influence of filter settings on signal quality. After reconstruction of the left atrium by three-dimensional atriography, baseline PV potentials (PVP) were recorded consecutively with PVAC and Orbiter in 20 patients with paroxysmal AF. PVPs were compared and attributed to predefined anatomical PV segments. Ablation was performed in 80 PVs using the PVAC. If isolation of the PVs was assumed, signal assessment of each PV was repeated with the Orbiter. If residual PV potentials could be uncovered, different filter settings were tested to improve mapping quality of the PVAC. Ablation was continued until complete PV isolation (PVI) was confirmed with the Orbiter. Baseline mapping demonstrated a good correlation between the Orbiter and PVAC. Mapping accuracy using the PVAC for mapping and ablation was 94% (74 of 79 PVs). Additional mapping with the Orbiter improved the PV isolation rate to 99%. Adjustment of filter settings failed to improve quality of the PV signals compared with standard filter settings. Using the PVAC as a stand-alone strategy for mapping and ablation, one should be aware that in some cases, different signal morphology mimics PVI isolation. Adjustment of filter settings failed to improve signal quality. The use of an additional mapping catheter is recommended to become familiar with the particular signal morphology during the first PVAC cases or whenever there is a doubt about successful isolation of the pulmonary veins.

Microbiological, chemical and physical quality of drinking water for commercial turkeys: a cross-sectional study.

PubMed

Di Martino, G; Piccirillo, A; Giacomelli, M; Comin, D; Gallina, A; Capello, K; Buniolo, F; Montesissa, C; Bonfanti, L

2018-04-17

Drinking water for poultry is not subject to particular microbiological, chemical and physical requirements, thereby representing a potential transmission route for pathogenic microorganisms and contaminants and/or becoming unsuitable for water-administered medications. This study assessed the microbiological, chemical and physical drinking water quality of 28 turkey farms in North-Eastern Italy: 14 supplied with tap water (TW) and 14 with well water (WW). Water salinity, hardness, pH, ammonia, sulphate, phosphate, nitrate, chromium, copper and iron levels were also assessed. Moreover, total bacterial count at 22°C, presence and enumeration of Enterococcus spp. and E. coli, presence of Salmonella spp. and Campylobacter spp. were quantified. A water sample was collected in winter and in summer at 3 sampling sites: the water source (A), the beginning (B) and the end (C) of the nipple line (168 samples in total). Chemical and physical quality of both TW and WW sources was mostly within the limits of TW for humans. However, high levels of hardness and iron were evidenced in both sources. In WW vs. TW, sulphate and salinity levels were significantly higher, whilst pH and nitrate levels were significantly lower. At site A, microbiological quality of WW and TW was mostly within the limit of TW for humans. However, both sources had a significantly lower microbiological quality at sites B and C. Salmonella enterica subsp. enterica serotype Kentucky was isolated only twice from WW. Campylobacter spp. were rarely isolated (3.6% of farms); however, Campylobacter spp. farm-level prevalence by real-time PCR was up to 43% for both water sources. Winter posed at higher risk than summer for Campylobacter spp. presence in water, whereas no significant associations were found with water source, site, recirculation system, and turkey age. Low salinity and high hardness were significant risk factors for C. coli and C. jejuni presence, respectively. These results show the need of improving sanitization of drinking water pipelines for commercial turkeys.

Global transcriptomic profiling using small volumes of whole blood: a cost-effective method for translational genomic biomarker identification in small animals.

PubMed

Fricano, Meagan M; Ditewig, Amy C; Jung, Paul M; Liguori, Michael J; Blomme, Eric A G; Yang, Yi

2011-01-01

Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total RNA samples were further processed using the NuGEN Ovation Whole Blood Solution system and cDNA was hybridized to Affymetrix Rat Genome 230 2.0 Arrays. The microarray QC parameters using RNA isolated with the QSI method were within the acceptable range for microarray analysis. The transcriptomic profiles were highly correlated with those using RNA isolated with the PAXgene method and were consistent with expected LPS-induced inflammatory responses. The present study demonstrated that the QSI method coupled with NuGEN Ovation Whole Blood Solution system is cost-effective and particularly suitable for transcriptomic profiling of minimal volumes of whole blood, typical of those obtained with small animal species.

Seismic Motion Stability, Measurement and Precision Control.

DTIC Science & Technology

1979-12-01

tiltmeter . Tilt was corrected by changing air pressure in one bank of isolators to maintain the reference tiltmeter at null well within the 0.1 arcsecond...frequency rotations (0-0.1 Hz), a high quality, two-axis tiltmeter is used. The azimuth orientation angle could be measured with a four-position gyro...compassing system with considerably less accuracy than the tiltmeters . However, it would provide a continuous automatic azimuth determination update every

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

PubMed

Hausmann, Bela; Pjevac, Petra; Schreck, Katharina; Herbold, Craig W; Daims, Holger; Wagner, Michael; Loy, Alexander

2018-01-25

The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum , including genes for sulfur oxidation. Copyright © 2018 Hausmann et al.

Isolation of PCR quality microbial community DNA from heavily contaminated environments.

PubMed

Gunawardana, Manjula; Chang, Simon; Jimenez, Abraham; Holland-Moritz, Daniel; Holland-Moritz, Hannah; La Val, Taylor P; Lund, Craig; Mullen, Madeline; Olsen, John; Sztain, Terra A; Yoo, Jennifer; Moss, John A; Baum, Marc M

2014-07-01

Asphalts, biochemically degraded oil, contain persistent, water-soluble compounds that pose a significant challenge to the isolation of PCR quality DNA. The adaptation of existing DNA purification protocols and commercial kits proved unsuccessful at overcoming this hurdle. Treatment of aqueous asphalt extracts with a polyamide resin afforded genomic microbial DNA templates that could readily be amplified by PCR. Physicochemically distinct asphalt samples from five natural oil seeps successfully generated the expected 291 bp amplicons targeting a region of the 16S rRNA gene, illustrating the robustness of the method. DNA recovery yields were in the 50-80% range depending on how the asphalt sample was seeded with exogenous DNA. The scope of the new method was expanded to include soil with high humic acid content. DNA from soil samples spiked with a range of humic acid concentrations was extracted with a commercial kit followed by treatment with the polyamide resin. The additional step significantly improved the purity of the DNA templates, especially at high humic acid concentrations, based on qPCR analysis of the bacterial 16S rRNA genes. The new method has the advantages of being inexpensive, simple, and rapid and should provide a valuable addition to protocols in the field of petroleum and soil microbiology. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, isolation and purification of [11C]-choline

PubMed Central

Jadwiński, Michał; Chmura, Agnieszka; Gorczewski, Kamil; Sokół, Maria

2016-01-01

[11C]-choline is an effective PET tracer used for imaging of neoplastic lesions and metastases of the prostate cancer. However, its production can be a challenge for manufacturers, as it has not yet been described in Polish or European pharmacopoeia. In this study the technical aspects of [11C]-choline production are described and detailed process parameters are provided. The quality control procedures for releasing [11C]-choline as solutio iniectabilis are also presented. The purity and quality of the radiopharmaceutical obtained according to the proposed method were find to be high enough to safely administrate the radiopharmaceutical to patients. Application of an automated synthesizer makes it possible to carry out the entire process of [11C]-choline production, isolation and purification within 20 minutes. It is crucial to maintain all aspects of the process as short as possible, since the decay half-time of carbon-11 is 20.4 minutes. The resulting radiopharmaceutical is sterile and pyrogen-free and of a high chemical, radiochemical, and radionuclide purity proved by chromatographic techniques. The yield of the process is up to 20%. [11C]-choline PET scanning can be used as accurate and effective diagnostic tool in all centers equipped with [11C]-target containing cyclotron. PMID:27660552

Defining geo-habitats for groundwater ecosystem assessments: an example from England and Wales (UK)

NASA Astrophysics Data System (ADS)

Weitowitz, Damiano C.; Maurice, Louise; Lewis, Melinda; Bloomfield, John P.; Reiss, Julia; Robertson, Anne L.

2017-12-01

Groundwater ecosystems comprising micro-organisms and metazoans provide an important contribution to global biodiversity. Their complexity depends on geology, which determines the physical habitat available, and the chemical conditions within it. Despite this, methods of classifying groundwater habitats using geological data are not well established and researchers have called for higher resolution habitat frameworks. A novel habitat typology for England and Wales (UK) is proposed, which distinguishes 11 geological habitats (geo-habitats) on hydrogeological principles and maps their distribution. Hydrogeological and hydrochemical data are used to determine the characteristics of each geo-habitat, and demonstrate their differences. Using these abiotic parameters, a new method to determine abiotic habitat quality is then developed. The geo-habitats had significantly different characteristics, validating the classification system. All geo-habitats were highly heterogeneous, containing both high quality habitat patches that are likely to be suitable for fauna, and areas of low quality that may limit faunal distributions. Karstic and porous habitats generally were higher quality than fractured habitats. Overall, 70% of England and Wales are covered by lower quality fractured habitats, with only 13% covered by higher quality habitats. The main areas of high quality habitats occur in central England as north-south trending belts, possibly facilitating dispersal along this axis. They are separated by low quality geo-habitats that may prevent east-west dispersal of fauna. In south-west England and Wales suitable geo-habitats occur as small isolated patches. Overall, this paper provides a new national-scale typology that is adaptable for studies in other geographic areas.

Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.

PubMed

Zischka, Melanie; Künne, Carsten T; Blom, Jochen; Wobser, Dominique; Sakιnç, Türkân; Schmidt-Hohagen, Kerstin; Dabrowski, P Wojtek; Nitsche, Andreas; Hübner, Johannes; Hain, Torsten; Chakraborty, Trinad; Linke, Burkhard; Goesmann, Alexander; Voget, Sonja; Daniel, Rolf; Schomburg, Dietmar; Hauck, Rüdiger; Hafez, Hafez M; Tielen, Petra; Jahn, Dieter; Solheim, Margrete; Sadowy, Ewa; Larsen, Jesper; Jensen, Lars B; Ruiz-Garbajosa, Patricia; Quiñones Pérez, Dianelys; Mikalsen, Theresa; Bender, Jennifer; Steglich, Matthias; Nübel, Ulrich; Witte, Wolfgang; Werner, Guido

2015-03-12

Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type. We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro). Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L.

PubMed

Doležel, J; Cíhalíková, J; Lucretti, S

1992-08-01

A new method is described for the isolation of large quantities of Vicia faba metaphase chromosomes. Roots were treated with 2.5 mM hydroxyurea for 18 h to accumulate meristem tip cells at the G1/S interface. After release from the block, the cells re-entered the cell cycle with a high degree of synchrony. A treatment with 2.5 μM amiprophos-methyl (APM) was used to accumulate mitotic cells in metaphase. The highest metaphase index (53.9%) was achieved when, 6 h after the release from the hydroxyurea block, the roots were exposed to APM for 4 h. The chromosomes were released from formaldehyde-fixed root tips by chopping with a scalpel in LB01 lysis buffer. Both the quality and the quantity of isolated chromosomes, examined microscopically and by flow cytometry, depended on the extent of the fixation. The best results were achieved after fixation with 6% formaldehyde for 30 min. Under these conditions, 1 · 10(6) chromosomes were routinely obtained from 30 root tips. The chromosomes were morphologically intact and suitable both for high-resolution chromosome studies and for flow-cytometric analysis and sorting. After the addition of hexylene glycol, the chromosome suspensions could be stored at 4° C for six months without any signs of deterioration.

Genotypic and phenotypic diversity of Alicyclobacillus acidocaldarius isolates.

PubMed

Félix-Valenzuela, L; Guardiola-Avila, I; Burgara-Estrella, A; Ibarra-Zavala, M; Mata-Haro, V

2015-10-01

The fruit juice industry recognizes Alicyclobacillus as a major quality control target micro-organism. In this study, we analysed 19 bacterial isolates to identify Alicyclobacillus species by polymerase chain reaction (PCR) and sequencing analyses. Phenotypic and genomic diversity among isolates were investigated by API 50CHB system and ERIC-PCR (enterobacterial repetitive intergenic consensus-PCR) respectively. All bacterial isolates were identified as Alicyclobacillus acidocaldarius, and almost all showed identical DNA sequences according to their 16S rRNA (rDNA) gene partial sequences. Only few carbohydrates were fermented by A. acidocaldarius isolates, and there was little variability in the biochemical profile. Genotypic fingerprinting of the A. acidocaldarius isolates showed high diversity, and clusters by ERIC-PCR were distinct to those obtained from the 16S rRNA gene phylogenetic tree. There was no correlation between phenotypic and genotypic variability in the A. acidocaldarius isolates analysed in this study. Detection of Alicyclobacillus strains is imperative in fruit concentrates and juices due to the production of guaiacol. Identification of the genera originates rejection of the product by processing industry. However, not all the Alicyclobacillus species are deteriorative and hence the importance to differentiate among them. In this study, partial 16S ribosomal RNA sequence alignment allowed the differentiation of species. In addition, ERIC-PCR was introduced for the genotypic characterization of Alicyclobacillus, as an alternative for differentiation among isolates from the same species. © 2015 The Society for Applied Microbiology.

Evaluation of Bacillus spp. as dough starters for Adhirasam - A traditional rice based fermented food of Southern India.

PubMed

Anisha, Anvar Hussain Noorul; Anandham, Rangasamy; Kwon, Soon Woo; Gandhi, Pandiyan Indira; Gopal, Nellaiappan Olaganathan

2015-01-01

Adhirasam is a cereal based, doughnut shaped, deep fried dessert consumed in the southern regions of India. The dough used to prepare adhirasam is fermented and contains rice flour and jaggery. The aim of the present study was to characterize the cultivable bacteria associated with this fermented dough and to identify a suitable starter culture for the production of quality adhirasam. In total, one hundred and seventy bacterial isolates were recovered from de Man Rogosa Sharp (MRS) agar, nutrient agar, lysogeny agar and tryptic soy agar media. Out of the 170 bacterial isolates, sixteen isolates were selected based on their ability to tolerate glucose and sucrose. All the bacterial isolates tolerated 15% glucose and 30% sucrose. Analyses of 16S rDNA gene sequences of the bacterial isolates showed that the dominant cultivable bacteria were members of the genus Bacillus. These strains were further used as starters and tested for their ability to ferment rice flour with jaggery to produce adhirasam dough. Organoleptic evaluation was carried out to choose the best starter strain. Adhirasam prepared from Bacillus subtilis isolates S4-P11, S2-G2-A1 and S1-G15, Bacillus tequilensis isolates S2-H16, S3-P9, S3-G10 and Bacillus siamensis isolate S2-G13 were highly acceptable to consumers. Adhirasam prepared using these starter cultures had superior product characteristics such as softness in texture, flavor and enhanced aroma and sweet taste.

Comparison of methods for cultivation and isolation of Chlamydia trachomatis.

PubMed Central

Benes, S; McCormack, W M

1982-01-01

McCoy cells treated with cycloheximide, iododeoxyuridine, and DEAE-dextran and untreated McCoy cells were inoculated with two stock strains of Chlamydia trachomatis and with 231 urethral specimens from men, 53 (23%) of which contained C. trachomatis. Isolation rates, number and quality of inclusions, and quality of the cell monolayers were compared. There were no significant differences between the isolation rates in the four systems, although the most isolations were made in the untreated and cycloheximide-treated cells. Cycloheximide-treated cells produced, from both the clinical specimens and the two stock strains, significantly more inclusions than any of the other systems. The monolayer of the cycloheximide-treated cells and the inclusions that grew in these cells were optimal for examination and detection of C. trachomatis. PMID:6185530

Rational quality assessment procedure for less-investigated herbal medicines: Case of a Congolese antimalarial drug with an analytical report.

PubMed

Tshitenge, Dieudonné Tshitenge; Ioset, Karine Ndjoko; Lami, José Nzunzu; Ndelo-di-Phanzu, Josaphat; Mufusama, Jean-Pierre Koy Sita; Bringmann, Gerhard

2016-04-01

Herbal medicines are the most globally used type of medical drugs. Their high cultural acceptability is due to the experienced safety and efficiency over centuries of use. Many of them are still phytochemically less-investigated, and are used without standardization or quality control. Choosing SIROP KILMA, an authorized Congolese antimalarial phytomedicine, as a model case, our study describes an interdisciplinary approach for a rational quality assessment of herbal drugs in general. It combines an authentication step of the herbal remedy prior to any fingerprinting, the isolation of the major constituents, the development and validation of an HPLC-DAD analytical method with internal markers, and the application of the method to several batches of the herbal medicine (here KILMA) thus permitting the establishment of a quantitative fingerprint. From the constitutive plants of KILMA, acteoside, isoacteoside, stachannin A, and pectolinarigenin-7-O-glucoside were isolated, and acteoside was used as the prime marker for the validation of an analytical method. This study contributes to the efforts of the WHO for the establishment of standards enabling the analytical evaluation of herbal materials. Moreover, the paper describes the first phytochemical and analytical report on a marketed Congolese phytomedicine. Copyright © 2016 Elsevier B.V. All rights reserved.

DNA cards: determinants of DNA yield and quality in collecting genetic samples for pharmacogenetic studies.

PubMed

Mas, Sergi; Crescenti, Anna; Gassó, Patricia; Vidal-Taboada, Jose M; Lafuente, Amalia

2007-08-01

As pharmacogenetic studies frequently require establishment of DNA banks containing large cohorts with multi-centric designs, inexpensive methods for collecting and storing high-quality DNA are needed. The aims of this study were two-fold: to compare the amount and quality of DNA obtained from two different DNA cards (IsoCode Cards or FTA Classic Cards, Whatman plc, Brentford, Middlesex, UK); and to evaluate the effects of time and storage temperature, as well as the influence of anticoagulant ethylenediaminetetraacetic acid on the DNA elution procedure. The samples were genotyped by several methods typically used in pharmacogenetic studies: multiplex PCR, PCR-restriction fragment length polymorphism, single nucleotide primer extension, and allelic discrimination assay. In addition, they were amplified by whole genome amplification to increase genomic DNA mass. Time, storage temperature and ethylenediaminetetraacetic acid had no significant effects on either DNA card. This study reveals the importance of drying blood spots prior to isolation to avoid haemoglobin interference. Moreover, our results demonstrate that re-isolation protocols could be applied to increase the amount of DNA recovered. The samples analysed were accurately genotyped with all the methods examined herein. In conclusion, our study shows that both DNA cards, IsoCode Cards and FTA Classic Cards, facilitate genetic and pharmacogenetic testing for routine clinical practice.

The impact of social isolation on the health status and health-related quality of life of older people.

PubMed

Hawton, Annie; Green, Colin; Dickens, Andy P; Richards, Suzanne H; Taylor, Rod S; Edwards, Rachel; Greaves, Colin J; Campbell, John L

2011-02-01

To investigate for socially isolated older people, and older people at risk of social isolation: (1) health status and health-related quality of life (HRQL); (2) the relationship between social isolation and health status/HRQL; (3) the relationship between two alternative measures of health status/HRQL. Older people at risk of social isolation (n = 393) completed the EQ-5D and the SF-12. Multiple regression analyses were performed to examine the relationship between levels of social isolation and health status/HRQL, controlling for demographic/clinical characteristics. The agreement between EQ-5D and SF-6D (SF-12) scores was explored using descriptive psychometric techniques. Health status and health state values were much lower than UK general population age-matched norms. After controlling for depression, physical co-morbidities, age, gender, living alone status, employment and accommodation, social isolation was significantly associated, to a degree that was clinically relevant, with EQ-5D DSI, SF-6D (SF-12) and SF-12 MCS scores. The potential for ceiling effects on the EQ-5D with this population was identified. This work highlights the burden that social isolation may have on the health and well-being of older people. The potential HRQL gains from addressing social isolation may be considerable, with those at risk of social isolation also a key target group.

BI-ground microstrip array coil vs. conventional microstrip array coil for mouse imaging at 7 tesla

NASA Astrophysics Data System (ADS)

Hernández, Ricardo; Terrones, M. A. López; Jakob, P. M.

2012-10-01

At high field strengths, the need for more efficient high frequency coils has grown. Since the radiation losses and the interaction between coil and sample increase proportionally to field strength, the quality factor (Q) and the sensitivity of the coil decrease as consequence of these negative effects. Since Zhang et al proposed in 2001 a new surface coil based on the microstrip transmission line for high frequency, different Tx-Rx phased arrays based on this concept have been already introduced in animal and whole body systems at high field strengths, each of them with different modifications in order to get better field homogeneity, SNR or isolation between coil elements in the array. All these arrays for animals systems have been built for rat imaging. One of these modifications is called BI-Ground Microstrip Array Coil (BIGMAC). The implementation of a smaller two-channel BIGMAC design for mouse imaging is studied and its performance compared to a two-channel conventional Microstrip array at 7 Tesla, the higher isolation by using BIGMAC elements in comparison with conventional Microstrip elements is shown in this work.

A New Genetic Vaccine Platform Based on an Adeno-Associated Virus Isolated from a Rhesus Macaque ▿

PubMed Central

Lin, Jianping; Calcedo, Roberto; Vandenberghe, Luk H.; Bell, Peter; Somanathan, Suryanarayan; Wilson, James M.

2009-01-01

We created a hybrid adeno-associated virus (AAV) from two related rhesus macaque isolates, called AAVrh32.33, and evaluated it as a vaccine carrier for human immunodeficiency virus type 1 (HIV-1) and type A influenza virus antigens. The goal was to overcome the limitations of vaccines based on other AAVs, which generate dysfunctional T-cell responses and are inhibited by antibodies found in human sera. Injection of a Gag-expressing AAVrh32.33 vector into mice resulted in a high-quality CD8+ T-cell response. The resulting Gag-specific T cells express multiple cytokines at high levels, including interleukin-2, with many having memory phenotypes; a subsequent boost with an adenovirus vector yielded a brisk expansion of Gag-specific T cells. A priming dose of AAVrh32.33 led to high levels of Gag antibodies, which exceed levels found after injection of adenovirus vectors. Importantly, passive transfer of pooled human immunoglobulin into mice does not interfere with the efficacy of AAVrh32.33 expressing nucleoproteins from influenza virus, as measured by protection to a lethal dose of influenza virus, which is consistent with the very low seroprevalence to this virus in humans. Studies of macaques with vectors expressing gp140 from HIV-1 (i.e., with AAVrh32.33 as the prime and simian adenovirus type 24 as the boost) demonstrated results similar to those for mice with high-level and high-quality CD8+ T-cell responses to gp140 and high-titered neutralizing antibodies to homologous HIV-1. The biology of this novel AAV hybrid suggests that it should be a preferred genetic vaccine carrier, capable of generating robust T- and B-cell responses. PMID:19812149

The Microgravity Isolation Mount (MGIM): A Columbus facility for improving the microgravity quality of payloads

NASA Technical Reports Server (NTRS)

Owen, R. G.; Jones, D. I.; Owens, A. R.; Roberts, G.; Hadfield, P.

1992-01-01

The Microgravity Isolation Mount (MGIM) is a facility for providing active vibration isolation for sensitive experiments on the Columbus Attached Laboratory and the Columbus Free-Flying Laboratory. The facility is designed to be accommodated in a standard Columbus rack, and it iterfaces with existing rack utility services. The design is based on a non-contact strategy, whereby the payload 'floats' inside the rack, and its position is controlled by a number of magnetic actuators. The main advantage of using this non-contact strategy is the improved microgravity quality available. The overall design of the facility and a description of its elements are given.

Isolating and evaluating lactic acid bacteria strains for effectiveness on silage quality at low temperatures on the Tibetan Plateau.

PubMed

Wang, Siran; Yuan, Xianjun; Dong, Zhihao; Li, Junfeng; Shao, Tao

2017-11-01

Four lactic acid bacteria (LAB) strains isolated from straw silages on the Tibetan Plateau were characterized, and their effects on the fermentation quality of Italian ryegrass (Lolium multiflorum Lam.) at different temperatures (10°C, 15°C and 25°C) were studied. These LAB isolates were evaluated using the acids production ability test, morphological observation, Gram staining, physiological, biochemical and acid tolerance tests. All the isolates (M1, LM8, LO7 and LOG9) could grow at 5-20°C, pH 3.5-7.0 and NaCl (3.0%, 6.5%). Strains M1, LM8, LO7 and LOG9 were identified as Lactobacillus plantarum, L. coryniformis, Pediococcus pentosaceus and P. acidilactici, respectively, by sequencing 16S ribosomal DNA. The four isolates were added to Italian ryegrass for ensiling for 30 days at various temperatures. Compared with the corresponding control, inoculating with isolates M1, LM8 and LO7 could improve the silage quality of Italian ryegrass at low temperatures, indicated by significantly (P < 0.05) higher lactic acid (LA) contents and ratios of lactic acid/acetic acid (LA/AA), and significantly (P < 0.05) lower pH and ammonia nitrogen/total nitrogen (AN/TN). Compared with other isolates, LM8 performed better at 10°C and 15°C, indicated by the higher (P < 0.05) LA content and ratio of LA/AA, and the lower (P < 0.05) pH and AN/TN. © 2017 Japanese Society of Animal Science.

Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring.

PubMed

Chang, Yi; Tolani, Bhairavi; Nie, Xiuhong; Zhi, Xiuyi; Hu, Mu; He, Biao

2017-01-01

Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.

The morphology of islets within the porcine donor pancreas determines the isolation result: successful isolation of pancreatic islets can now be achieved from young market pigs.

PubMed

Krickhahn, Mareike; Bühler, Christoph; Meyer, Thomas; Thiede, Arnulf; Ulrichs, Karin

2002-01-01

Clinical islet allotransplantation has become an increasingly efficient "routine" therapy in recent years. Shortage of human donor organs leads to porcine pancreatic islets as a potential source for islet xenotransplantation. Yet it is still very difficult to isolate sufficient numbers of intact porcine islets, particularly from young market pigs. In the following study islets were successfully isolated from retired breeders [4806 +/- 720 islet equivalents per gram organ (IEQ/g); n = 25; 2-3 years old; RB] and also from young hybrid pigs [2868 +/- 260 IEQ/g; n = 65; 4-6 months old; HY] using LiberasePI and a modified version of Ricordi's digestion-filtration technique. As expected, isolations from RB showed significantly better results (p < 0.002). A retrospective histological analysis of almost all donor pancreases showed that the majority of organs from RB (80%) contained mainly large islets (diameter > 200 microm), in contrast to only 35% of all pancreases from HY. Remarkably, the islet size in situ, regardless whether detected in RB or HY, strongly determined the isolation result. A donor organ with predominantly large islets resulted in significantly higher numbers of IEQs compared with a donor organ with predominantly small islets [RB(Large Islets): 5680 +/- 3,318 IEQ/g (n= 20); RB(Small Islets): 1353 +/- 427 IEQ/g (n = 5); p < 0.02]. In addition, isolation results were strongly influenced by the quality of the LiberasePI batch, and therefore single batch testing is invariably required. Purification was performed using Ficoll or OptiPrep density gradient centrifugation manually or in the COBE cell processor. Although islet purity was highest when OptiPrep was used, final islet yields did not differ between the different purification methods. Our study demonstrates that islet size in situ is an extremely critical parameter for highly successful islet isolation; consequently, we are now performing a morphological screening of each donor organ prior to the isolation process. Under these conditions highly successful isolations can reliably be performed even from young market pigs.

The quality of our Nation's waters: water quality in the Denver Basin aquifer system, Colorado, 2003-05

USGS Publications Warehouse

Bauch, Nancy J.; Musgrove, MaryLynn; Mahler, Barbara J.; Paschke, Suzanne

2015-01-01

Availability and sustainability of groundwater in the Denver Basin aquifer system depend on water quantity and water quality. The Denver Basin aquifer system underlies about 7,000 square miles of the Great Plains in eastern Colorado and is the primary or sole source of water for domestic and public supply in many areas of the basin. Use of groundwater from the Denver Basin sandstone aquifers has been instrumental for development of the south Denver metropolitan area and other areas, but has resulted in a decline in water levels in some parts of the system. Human activities in many areas have adversely affected the quality of water in the aquifer system, especially the shallow parts. Groundwater in deeper parts of the system used for drinking water, once considered isolated from the effects of overlying land use, is increasingly vulnerable to contamination from human activities and geologic materials. Availability and sustainability of high-quality groundwater are vital to the economic health of the Denver Basin area.

Cottonseed protein derivatives as nutritional and functional supplements in food formulations.

PubMed

Cherry, J P; Berardi, L C; Zarins, Z M; Wadsworth, J I; Vinnett, C H

1978-01-01

Cottonseeds contain protein with desirable food functional and nutritional properties. Storage globulins make up most of the protein stored in cottonseed and can be separated into five fractions by gel filtration chromatography. Each fraction is distinguishable from the other by its amino acid and polyacrylamide gel electrophoretic properties. Proteins of cottonseed contribute greatly to the functional properties of emulsions, co-isolates, and texturized derivatives. For example, increasing the amount of high protein cottonseed flour in wheat suspensions from 2% to 10% improved the capacity (54-97 ml of oil) and viscosity (5,000-100,000+ cps) of emulsions. The 10% suspension formed emulsions with increasing oil capacity (84-100 ml) and viscosity (28,000-100,000+ cps) as the pH was adjusted from 4.5 to 9.5. Consistencies of the products ranged from that of salad dressing (low percent suspensions, or acid pH) to that of mayonnaise (high percent, or basic pH). These data were utilized to derive a multiple regression model to predict optimum use of cottonseed proteins in emulsions of varying consistencies. A coprecipitated isolate containing greater than 94% protein was prepared from a blend of cottonseed and peanut flours. Amino acid content of the co-isolate reflected that of the protein in the two flours of the composite. The co-isolate has lower gossypol level and improved color and functional properties than a cottonseed protein isolate. Storage protein isolate of cottonseed suspended in aqueous solution and heated with constant stirring forms a texturized product; the quality of the product depends on heat, pH, salt, and the quantity of nonstorage proteins. Protein and amino acid content of meat products were improved by the addition of the texturized protein of cottonseed.

[The comparison of selected virulence factors in Pseudomonas aeruginosa catheter isolates].

PubMed

Olejnízková, Katerina; Holá, Veronika

2012-05-01

Healthcare quality improvement brings about an increasing number of invasive diagnostic and therapeutic procedures and thus also an increasing number of high-risk patients prone to hospital infections. Pseudomonas aeruginosa is one of the most commonly isolated nosocomial species and the treatment of the infection is often long and problematic, with frequent recurrences. The pathogenesis of Pseudomonas infection is associated with a range of virulence factors. In the present study, 93 catheter isolates of Pseudomonas aeruginosa were screened for the biofilm formation, motility and secretion of selected extracellular products. A high rate of the strains tested were producers of hemolysins, LasB elastase, and pyoverdines (> 70%). The biofilm formation was detected in 80% of isolates and formation of aerated biofilm was present in 90% of isolates with a positive correlation found between the two types of biofilm formation (p = 0.00583; gamma = 0.551). All strains showed swarming motility, 95% of strains showed swimming motility, and 75% of strains showed twitching motility. Among the virulence factors studied, only pyocyanin and pyochelin were produced by a lower proportion of isolates (< 25%). A positive correlation was seen between the production of some extracellular molecules (pyochelin and pyocyanin, pyocyanin and LasB elastase, and LasB elastase and haemolysins), between biofilm formation and formation of aerated biofilm, and between formation of aerated biofilm and pigments (pyoverdine and pyocyanin) production. On the other hand, a negative correlation was found between biofilm production and LasB elastase production and between the production of biofilm under immersion and pigments (pyoverdine and pyocyanin) production. All correlations are significant at the level p = 0.05, with the correlation coefficient gamma > 0.50.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Bova, G Steven; Eltoum, Isam A; Kiernan, John A; Siegal, Gene P; Frost, Andra R; Best, Carolyn J M; Gillespie, John W; Su, Gloria H; Emmert-Buck, Michael R

2005-02-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications.

PubMed

Rodriguez-Canales, Jaime; Hanson, Jeffrey C; Hipp, Jason D; Balis, Ulysses J; Tangrea, Michael A; Emmert-Buck, Michael R; Bova, G Steven

2013-01-01

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high-quality, appropriately anatomically tagged scientific results. Improvement in this area will significantly increase life science quality and productivity. The chapter is divided into introduction, materials, protocols, and notes subheadings. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this chapter, readers are advised to read through the entire chapter first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.

Fluids and Materials Science Studies Utilizing the Microgravity-vibration Isolation Mount (MIM)

NASA Technical Reports Server (NTRS)

Herring, Rodney; Tryggvason, Bjarni; Duval, Walter

1998-01-01

Canada's Microgravity Sciences Program (MSP) is the smallest program of the ISS partners and so can participate in only a few, highly focused projects in order to make a scientific and technological impact. One focused project involves determining the effect of accelerations (g-jitter) on scientific measurements in a microgravity environment utilizing the Microgravity-vibration Isolation Mount (MIM). Many experiments share the common characteristic of having a fluid stage in their process. The quality of the experimental measurements have been expected to be affected by g-jitters which has lead the ISS program to include specifications to limit the level of acceleration allowed on a subset of experimental racks. From finite element analysis (FEM), the ISS structure will not be able to meet the acceleration specifications. Therefore, isolation systems are necessary. Fluid science results and materials science results show significant sensitivity to g-jitter. The work done to date should be viewed only as a first look at the issue of g-jitter sensitivity. The work should continue with high priority such that the international science community and the ISS program can address the requirement and settle on an agreed to overall approach as soon as possible.

Screening of Lactobacillus isolates from gastrointestinal tract of guinea fowl for probiotic qualities using in vitro tests to select species-specific probiotic candidates.

PubMed

Vineetha, P G; Tomar, S; Saxena, V K; Susan, C; Sandeep, S; Adil, K; Mukesh, K

2016-08-01

A total of 32 Lactobacillus isolates, 8 each from the crop (LGFCP1-LGFCP8), proventriculus (LGFP9-LGFP16), ileum (LGFI17-LGFI24) and caeca (LGFCM25-LGFCM32) were isolated from 25 adult guinea fowl (Pearl variety), 22-28 weeks of age, and characterised morphologically, physiologically, biochemically and by molecular methods. Isolates were screened for their probiotic quality using range of in vitro tests: aggregation test, cell surface hydrophobicity, resistance to bile salts and acidic conditions, enzymatic tests and coaggregation and antagonistic test. Based on in vitro test results and a novel scoring method, the two best isolates were selected and partial 16S rRNA sequencing was done. BLAST (Basic Local Alignment Search Tool) analysis of sequence of isolate LGFCP4 showed 99% genetic identity with Lactobacillus plantarum and LGFP16 with Lactobacillus reuteri. The study shows that these two microbial agents may be suitable as potential probiotic candidates in guinea fowl, as well as in a feed supplement for other poultry species.

Foodborne Pathogens Recovered from Ready-to-Eat Foods from Roadside Cafeterias and Retail Outlets in Alice, Eastern Cape Province, South Africa: Public Health Implications

PubMed Central

Nyenje, Mirriam E.; Odjadjare, Collins E.; Tanih, Nicoline F.; Green, Ezekiel; Ndip, Roland N.

2012-01-01

This study assessed the microbiological quality of various ready-to-eat foods sold in Alice, South Africa. Microbiological analysis was conducted on 252 samples which included vegetables, potatoes, rice, pies, beef and chicken stew. The isolates were identified using biochemical tests and the API 20E, API 20NE and API Listeria kits; results were analyzed using the one-way-ANOVA test. Bacterial growth was present in all the food types tested; high levels of total aerobic count were observed in vegetables, 6.8 ± 0.07 followed by rice, 6.7 ± 1.7 while pies had the lowest count (2.58 ± 0.24). Organisms isolated included: Listeria spp. (22%), Enterobacter spp. (18%), Aeromonas hydrophila (12%), Klebsiella oxytoca (8%), Proteus mirabilis (6.3%), Staphylococcus aureus (3.2%) and Pseudomonas luteola (2.4%). Interestingly, Salmonella spp. and Escherichia coli were not isolated in any of the samples. There was a statistically significant difference (p < 0.05) in the prevalence of foodborne pathogens from hygienic and unhygienic cafeterias. The results indicated that most of the ready-to-eat food samples examined in this study did not meet bacteriological quality standards, therefore posing potential risks to consumers. This should draw the attention of the relevant authorities to ensure that hygienic standards are improved to curtain foodborne infections. PMID:23066386

Widefield Imaging: Selected Strategies for Processing Light-Contaminated Data

NASA Astrophysics Data System (ADS)

Cannistra, Stephen A.

The beauty of nebulae, galaxies, and star clusters takes on new meaning when portrayed in a widefield view, where familiar objects that are commonly seen in isolation are now shown in relation to one another. Through the use of high quality, short focal length optics combined with large, commercially available CCD chips, it is possible to capture broad regions of sky that an older generation of astrophotographers could only dream of.

Supercritical fluid chromatography for separation and preparation of tautomeric 7-epimeric spiro oxindole alkaloids from Uncaria macrophylla.

PubMed

Yang, Wenzhi; Zhang, Yibei; Pan, Huiqin; Yao, Changliang; Hou, Jinjun; Yao, Shuai; Cai, Luying; Feng, Ruihong; Wu, Wanying; Guo, Dean

2017-02-05

Increasing challenge arising from configurational interconversion in aqueous solvent renders it rather difficult to isolate high-purity tautomeric reference standards and thus largely hinders the holistic quality control of traditional Chinese medicine (TCM). Spiro oxindole alkaloids (SOAs), as the markers for the medicinal Uncaria herbs, can easily isomerize in polar or aqueous solvent via a retro-Mannich reaction. In the present study, supercritical fluid chromatography (SFC) is utilized to separate and isolate two pairs of 7-epimeric SOAs, including rhynchophylline (R) and isorhynchophylline (IR), corynoxine (C) and corynoxine B (CB), from Uncaria macrophylla. Initially, the solvent that can stabilize SOA epimers was systematically screened, and acetonitrile was used to dissolve and as the modifier in SFC. Then, key parameters of ultra-high performance SFC (ultra-performance convergence chromatography, UPC 2 ), comprising stationary phase, additive in modifier, column temperature, ABPR pressure, and flow rate, were optimized in sequence. Two isocratic UPC 2 methods were developed on the achiral Torus 1-AA and Torus Diol columns, suitable for UV and MS detection, respectively. MCI gel column chromatography fractionated the U. macrophylla extract into two mixtures (R/IR and C/CB). Preparative SFC, using a Viridis Prep Silica 2-EP OBD column and acetonitrile-0.2% diethylamine in CO 2 as the mobile phase, was finally employed for compound purification. As a result, the purity of four SOA compounds was all higher than 95%. Different from reversed-phase HPLC, SFC, by use of water-free mobile phase (inert CO 2 and aprotic modifier), provides a solution to rapid analysis and isolation of tautomeric reference standards for quality control of TCM. Copyright © 2016 Elsevier B.V. All rights reserved.

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline.

PubMed

Wyllie, David H; Sanderson, Nicholas; Myers, Richard; Peto, Tim; Robinson, Esther; Crook, Derrick W; Smith, E Grace; Walker, A Sarah

2018-06-06

Contact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artefactual variation between M. tuberculosis isolates during routine next generation sequencing of Mycobacterium spp, we investigated its basis in 2,018 consecutive M. tuberculosis isolates. In the routine process used, clinical samples were decontaminated and inoculated into broth cultures; from positive broth cultures DNA was extracted, sequenced, reads mapped, and consensus sequences determined. We investigated the process of consensus sequence determination, which selects the most common nucleotide at each position. Having determined the high-quality read depth and depth of minor variants across 8,006 M. tuberculosis genomic regions, we quantified the relationship between the minor variant depth and the amount of non-Mycobacterial bacterial DNA, which originates from commensal microbes killed during sample decontamination. In the presence of non-Mycobacterial bacterial DNA, we found significant increases in minor variant frequencies of more than 1.5 fold in 242 regions covering 5.1% of the M. tuberculosis genome. Included within these were four high variation regions strongly influenced by the amount of non-Mycobacterial bacterial DNA. Excluding these four regions from pairwise distance comparisons reduced biologically implausible variation from 5.2% to 0% in an independent validation set derived from 226 individuals. Thus, we have demonstrated an approach identifying critical genomic regions contributing to clinically relevant artefactual variation in bacterial similarity searches. The approach described monitors the outputs of the complex multi-step laboratory and bioinformatics process, allows periodic process adjustments, and will have application to quality control of routine bacterial genomics. Copyright © 2018 Wyllie et al.

Modified salting-out method: high-yield, high-quality genomic DNA extraction from whole blood using laundry detergent.

PubMed

Nasiri, H; Forouzandeh, M; Rasaee, M J; Rahbarizadeh, F

2005-01-01

Different approaches have been used to extract DNA from whole blood. In most of these methods enzymes (such as proteinase K and RNAse A) or toxic organic solvents (such as phenol or guanidine isothiocyanate) are used. Since these enzymes are expensive, and most of the materials that are used routinely are toxic, it is desirable to apply an efficient DNA extraction procedure that does not require the use of such materials. In this study, genomic DNA was extracted by the salting-out method, but instead of using an analytical-grade enzyme and chemical detergents, as normally used for DNA isolation, a common laundry powder was used. Different concentrations of the powder were tested, and proteins were precipitated by NaCl-saturated distilled water. Finally, DNA precipitation was performed with the use of 96% ethanol. From the results, we conclude that the optimum concentration of laundry powder for the highest yield and purity of isolated DNA is 30 mg/mL. The procedure was optimized, and a final protocol is suggested. Following the same protocol, DNA was extracted from 100 blood samples, and their amounts were found to be >50 microg/mL of whole blood. The integrity of the DNA fragments was confirmed by agarose gel electrophoresis. Furthermore, the extracted DNA was used as a template for PCR reaction. The results obtained from PCR showed that the final solutions of extracted DNA did not contain any inhibitory material for the enzyme used in the PCR reaction, and indicated that the isolated DNA was of good quality. These results show that this method is simple, fast, safe, and cost-effective, and can be used in medical laboratories and research centers. Copyright 2005 Wiley-Liss, Inc.

Role of Bacterial Exopolysaccharides (EPS) in the Fate of the Oil Released during the Deepwater Horizon Oil Spill

PubMed Central

Gutierrez, Tony; Berry, David; Yang, Tingting; Mishamandani, Sara; McKay, Luke; Teske, Andreas; Aitken, Michael D.

2013-01-01

Halomonas species are recognized for producing exopolysaccharides (EPS) exhibiting amphiphilic properties that allow these macromolecules to interface with hydrophobic substrates, such as hydrocarbons. There remains a paucity of knowledge, however, on the potential of Halomonas EPS to influence the biodegradation of hydrocarbons. In this study, the well-characterized amphiphilic EPS produced by Halomonas species strain TG39 was shown to effectively increase the solubilization of aromatic hydrocarbons and enhance their biodegradation by an indigenous microbial community from oil-contaminated surface waters collected during the active phase of the Deepwater Horizon oil spill. Three Halomonas strains were isolated from the Deepwater Horizon site, all of which produced EPS with excellent emulsifying qualities and shared high (97-100%) 16S rRNA sequence identity with strain TG39 and other EPS-producing Halomonas strains. Analysis of pyrosequence data from surface water samples collected during the spill revealed several distinct Halomonas phylotypes, of which some shared a high sequence identity (≥97%) to strain TG39 and the Gulf spill isolates. Other bacterial groups comprising members with well-characterized EPS-producing qualities, such as Alteromonas , Colwellia and Pseudoalteromonas , were also found enriched in surface waters, suggesting that the total pool of EPS in the Gulf during the spill may have been supplemented by these organisms. Roller bottle incubations with one of the Halomonas isolates from the Deepwater Horizon spill site demonstrated its ability to effectively produce oil aggregates and emulsify the oil. The enrichment of EPS-producing bacteria during the spill coupled with their capacity to produce amphiphilic EPS is likely to have contributed to the ultimate removal of the oil and to the formation of oil aggregates, which were a dominant feature observed in contaminated surface waters. PMID:23826336

Bacterial Contamination of Boar Semen and its Relationship to Sperm Quality Preserved in Commercial Extender Containing Gentamicin Sulfate.

PubMed

Gączarzewicz, D; Udała, J; Piasecka, M; Błaszczyk, B; Stankiewicz, T

2016-09-01

This study was designed to determine the degree and type of bacterial contamination in boar semen (79 ejaculates from Large White and Landrace boars) and its consequences for sperm quality during storage (27 extended semen samples, 16°C for five days) under practical conditions of artificial insemination (AI). The results revealed the presence of aerobic bacteria in 99% of the ejaculates (from 80 to 370 ×106 colony-forming units/mL). Most of the ejaculates contained two or three bacterial contaminants, while the Staphylococcus, Streptococcus, and Pseudomonas bacterial genera were most frequently isolated. Also detected were Enterobacter spp., Bacillus spp., Proteus spp., Escherichia coli, P. fluorescens, and P. aeruginosa. In general, the growth of certain bacterial types isolated prior to semen processing (Enterobacter spp., E. coli, P. fluorescens, and P. aeruginosa) was not discovered on different days of storage, but fluctuations (with a tendency towards increases) were found in the frequencies of Bacillus spp., Pseudomonas spp., and Staphylococcus spp. isolates up to the end of storage. Semen preserved for five days exhibited decreases in sperm motility and increases in the average number of total aerobic bacteria; this was associated with sperm agglutination, plasma membrane disruption, and acrosome damage. We inferred that, due to the different degrees and types of bacterial contaminants in the boar ejaculates, the inhibitory activity of some antimicrobial agents used in swine extenders (such as gentamicin sulfate) may be limited. Because such agents can contribute to the overgrowth of certain aerobic bacteria and a reduction in the quality of stored semen, procedures with high standards of hygiene and microbiological control should be used when processing boar semen.

Evaluation of the effects of different liquid inoculant formulations on the survival and plant-growth-promoting efficiency of Rhodopseudomonas palustris strain PS3.

PubMed

Lee, Sook-Kuan; Lur, Huu-Sheng; Lo, Kai-Jiun; Cheng, Kuan-Chen; Chuang, Chun-Chao; Tang, Shiueh-Jung; Yang, Zhi-Wei; Liu, Chi-Te

2016-09-01

Biofertilizers can help improve soil quality, promote crop growth, and sustain soil health. The photosynthetic bacterium Rhodopseudomonas palustris strain PS3 (hereafter, PS3), which was isolated from Taiwanese paddy soil, can not only exert beneficial effects on plant growth but also enhance the efficiency of nutrient uptake from applied fertilizer. To produce this elite microbial isolate for practical use, product development and formulation are needed to permit the maintenance of the high quality of the inoculant during storage. The aim of this study was to select a suitable formulation that improves the survival and maintains the beneficial effects of the PS3 inoculant. Six additives (alginate, polyethylene glycol [PEG], polyvinylpyrrolidone-40 [PVP], glycerol, glucose, and horticultural oil) were used in liquid-based formulations, and their capacities for maintaining PS3 cell viability during storage in low, medium, and high temperature ranges were evaluated. Horticultural oil (0.5 %) was chosen as a potential additive because it could maintain a relatively high population and conferred greater microbial vitality under various storage conditions. Furthermore, the growth-promoting effects exerted on Chinese cabbage by the formulated inoculants were significantly greater than those of the unformulated treatments. The fresh and dry weights of the shoots were significantly increased, by 10-27 and 22-40 %, respectively. Horticultural oil is considered a safe, low-cost, and easy-to-process material, and this formulation would facilitate the practical use of strain PS3 in agriculture.

Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado.

PubMed

Souza, H A V; Muller, L A C; Brandão, R L; Lovato, M B

2012-03-22

Dimorphandra mollis (Leguminosae), known as faveiro and fava d'anta, is a tree that is widely distributed throughout the Brazilian Cerrado (a savanna-like biome). This species is economically valuable and has been extensively exploited because its fruits contain the flavonoid rutin, which is used to produce medications for human circulatory diseases. Knowledge about its genetic diversity is needed to guide decisions about the conservation and rational use of this species in order to maintain its diversity. DNA extraction is an essential step for obtaining good results in a molecular analysis. However, DNA isolation from plants is usually compromised by excessive contamination by secondary metabolites. DNA extraction of D. mollis, mainly from mature leaves, results in a highly viscous mass that is difficult to handle and use in techniques that require pure DNA. We tested four protocols for plant DNA extraction that can be used to minimize problems such as contamination by polysaccharides, which is more pronounced in material from mature leaves. The protocol that produced the best DNA quality initially utilizes a sorbitol buffer to remove mucilaginous polysaccharides. The macerated leaf material is washed with this buffer until there is no visible mucilage in the sample. This protocol is adequate for DNA extraction both from young and mature leaves, and could be useful not only for D. mollis but also for other species that have high levels of polysaccharide contamination during the extraction process.

Wavelet methodology to improve single unit isolation in primary motor cortex cells

PubMed Central

Ortiz-Rosario, Alexis; Adeli, Hojjat; Buford, John A.

2016-01-01

The proper isolation of action potentials recorded extracellularly from neural tissue is an active area of research in the fields of neuroscience and biomedical signal processing. This paper presents an isolation methodology for neural recordings using the wavelet transform (WT), a statistical thresholding scheme, and the principal component analysis (PCA) algorithm. The effectiveness of five different mother wavelets was investigated: biorthogonal, Daubachies, discrete Meyer, symmetric, and Coifman; along with three different wavelet coefficient thresholding schemes: fixed form threshold, Stein’s unbiased estimate of risk, and minimax; and two different thresholding rules: soft and hard thresholding. The signal quality was evaluated using three different statistical measures: mean-squared error, root-mean squared, and signal to noise ratio. The clustering quality was evaluated using two different statistical measures: isolation distance, and L-ratio. This research shows that the selection of the mother wavelet has a strong influence on the clustering and isolation of single unit neural activity, with the Daubachies 4 wavelet and minimax thresholding scheme performing the best. PMID:25794461

Quality of Life and Quality of Support for People with Severe Intellectual Disability and Complex Needs

ERIC Educational Resources Information Center

Beadle-Brown, J.; Leigh, J.; Whelton, B.; Richardson, L.; Beecham, J.; Baumker, T.; Bradshaw, J.

2016-01-01

Background: People with severe and profound intellectual disabilities often spend substantial time isolated and disengaged. The nature and quality of the support appears to be important in determining quality of life. Methods: Structured observations and staff questionnaires were used to explore the quality of life and quality of support for 110…

Aeromonas hydrophila and Aeromonas veronii Predominate among Potentially Pathogenic Ciprofloxacin- and Tetracycline-Resistant Aeromonas Isolates from Lake Erie

PubMed Central

Shinko, Jasmine; Augustyniak, Alexander; Gee, Christopher; Andraso, Greg

2014-01-01

Members of the genus Aeromonas are ubiquitous in nature and have increasingly been implicated in numerous diseases of humans and other animal taxa. Although some species of aeromonads are human pathogens, their presence, density, and relative abundance are rarely considered in assessing water quality. The objectives of this study were to identify Aeromonas species within Lake Erie, determine their antibiotic resistance patterns, and assess their potential pathogenicity. Aeromonas strains were isolated from Lake Erie water by use of Aeromonas selective agar with and without tetracycline and ciprofloxacin. All isolates were analyzed for hemolytic ability and cytotoxicity against human epithelial cells and were identified to the species level by using 16S rRNA gene restriction fragment length polymorphisms and phylogenetic analysis based on gyrB gene sequences. A molecular virulence profile was identified for each isolate, using multiplex PCR analysis of six virulence genes. We demonstrated that Aeromonas comprised 16% of all culturable bacteria from Lake Erie. Among 119 Aeromonas isolates, six species were identified, though only two species (Aeromonas hydrophila and A. veronii) predominated among tetracycline- and ciprofloxacin-resistant isolates. Additionally, both of these species demonstrated pathogenic phenotypes in vitro. Virulence gene profiles demonstrated a high prevalence of aerolysin and serine protease genes among A. hydrophila and A. veronii isolates, a genetic profile which corresponded with pathogenic phenotypes. Together, our findings demonstrate increased antibiotic resistance among potentially pathogenic strains of aeromonads, illustrating an emerging potential health concern. PMID:24242249

Application of Cell-Specific Isolation to the Study of Dopamine Signaling in Drosophila

PubMed Central

Iyer, Eswar Prasad R.; Iyer, Srividya Chandramouli; Cox, Daniel N.

2014-01-01

Dopamine neurotransmission accounts for a number of important brain functions across species including memory formation, the anticipation of reward, cognitive facilities, and drug addiction. Despite this functional significance, relatively little is known of the cellular pathways associated with drug-induced molecular adaptations within individual neurons. Due to its genetic tractability, simplicity, and economy of scale, Drosophila melanogaster has become an important tool in the study of neurological disease states, including drug addiction. To facilitate high-resolution functional analyses of dopamine signaling, it is highly advantageous to obtain genetic material, such as RNA or protein, from a homogeneous cell source. This process can be particularly challenging in most organisms including small model system organisms such as Drosophila melanogaster. Magnetic bead-based cell sorting has emerged as a powerful tool that can be used to isolate select populations of cells, from a whole organism or tissue such as the brain, for genomic as well as proteomic expression profiling. Coupled with the temporal and spatial specificity of the GAL4/UAS system, we demonstrate the application of magnetic bead-based cell sorting towards the isolation of dopaminergic neurons from the Drosophila adult nervous system. RNA derived from these neurons is of high quality and suitable for downstream applications such as microarray expression profiling or quantitative rtPCR. The versatility of this methodology stems from the fact that the cell-specific isolation method employed can be used under a variety of experimental conditions designed to survey molecular adaptations in dopamine signaling neurons including in response to drugs of abuse. PMID:23296786

Evaluation of CLSI M44-A2 Disk Diffusion and Associated Breakpoint Testing of Caspofungin and Micafungin Using a Well-Characterized Panel of Wild-Type and fks Hot Spot Mutant Candida Isolates▿

PubMed Central

Arendrup, Maiken Cavling; Park, Steven; Brown, Steven; Pfaller, Michael; Perlin, David S.

2011-01-01

Disk diffusion testing has recently been standardized by the CLSI, and susceptibility breakpoints have been established for several antifungal compounds. For caspofungin, 5-μg disks are approved, and for micafungin, 10-μg disks are under evaluation. We evaluated the performances of caspofungin and micafungin disk testing using a panel of Candida isolates with and without known FKS echinocandin resistance mechanisms. Disk diffusion and microdilution assays were performed strictly according to CLSI documents M44-A2 and M27-A3. Eighty-nine clinical Candida isolates were included: Candida albicans (20 isolates/10 mutants), C. glabrata (19 isolates/10 mutants), C. dubliniensis (2 isolates/1 mutant), C. krusei (16 isolates/3 mutants), C. parapsilosis (14 isolates/0 mutants), and C. tropicalis (18 isolates/4 mutants). Quality control strains were C. parapsilosis ATCC 22019 and C. krusei ATCC 6258. The correlations between zone diameters and MIC results were good for both compounds, with identical susceptibility classifications for 93.3% of the isolates by applying the current CLSI breakpoints. However, the numbers of fks hot spot mutant isolates misclassified as being susceptible (S) (very major errors [VMEs]) were high (61% for caspofungin [S, ≥11 mm] and 93% for micafungin [S, ≥14 mm]). Changing the disk diffusion breakpoint to S at ≥22 mm significantly improved the discrimination. For caspofungin, 1 VME was detected (a C. tropicalis isolate with an F76S substitution) (3.5%), and for micafungin, 10 VMEs were detected, the majority of which were for C. glabrata (8/10). The broadest separation between zone diameter ranges for wild-type (WT) and mutant isolates was seen for caspofungin (6 to 12 mm versus −4 to 7 mm). In conclusion, caspofungin disk diffusion testing with a modified breakpoint led to excellent separation between WT and mutant isolates for all Candida species. PMID:21357293

Pure zero-dimensional Cs4PbBr6 single crystal rhombohedral microdisks with high luminescence and stability.

PubMed

Zhang, Haihua; Liao, Qing; Wu, Yishi; Chen, Jianwei; Gao, Qinggang; Fu, Hongbing

2017-11-08

Zero-dimensional (0D) perovskite Cs 4 PbBr 6 has been speculated to be an efficient solid-state emitter, exhibiting strong luminescense on achieving quantum confinement. Although several groups have reported strong green luminescence from Cs 4 PbBr 6 powders and nanocrystals, doubts that the origin of luminescence comes from Cs 4 PbBr 6 itself or CsPbBr 3 impurities have been a point of controversy in recent investigations. Herein, we developed a facile one-step solution self-assembly method to synthesize pure zero-dimensional rhombohedral Cs 4 PbBr 6 micro-disks (MDs) with a high PLQY of 52% ± 5% and photoluminescence full-width at half maximum (FWHM) of 16.8 nm. The obtained rhombohedral MDs were high quality single-crystalline as demonstrated by XRD and SAED patterns. We demonstrated that Cs 4 PbBr 6 MDs and CsPbBr 3 MDs were phase-separated from each other and the strong green emission comes from Cs 4 PbBr 6 . Power and temperature dependence spectra evidenced that the observed strong green luminescence of pure Cs 4 PbBr 6 MDs originated from direct exciton recombination in the isolated octahedra with a large binding energy of 303.9 meV. Significantly, isolated PbBr 6 4- octahedra separated by a Cs + ion insert in the crystal lattice is beneficial to maintaining the structural stability, depicting superior thermal and anion exchange stability. Our study provides an efficient approach to obtain high quality single-crystalline Cs 4 PbBr 6 MDs with highly efficient luminescence and stability for further optoelectronic applications.

A network extension of species occupancy models in a patchy environment applied to the Yosemite toad (Anaxyrus canorus)

USGS Publications Warehouse

Berlow, Eric L.; Knapp, Roland A.; Ostoja, Steven M.; Williams, Richard J.; McKenny, Heather; Matchett, John R.; Guo, Qinghau; Fellers, Gary M.; Kleeman, Patrick; Brooks, Matthew L.; Joppa, Lucas

2013-01-01

A central challenge of conservation biology is using limited data to predict rare species occurrence and identify conservation areas that play a disproportionate role in regional persistence. Where species occupy discrete patches in a landscape, such predictions require data about environmental quality of individual patches and the connectivity among high quality patches. We present a novel extension to species occupancy modeling that blends traditionalpredictions of individual patch environmental quality with network analysis to estimate connectivity characteristics using limited survey data. We demonstrate this approach using environmental and geospatial attributes to predict observed occupancy patterns of the Yosemite toad (Anaxyrus (= Bufo) canorus) across >2,500 meadows in Yosemite National Park (USA). A. canorus, a Federal Proposed Species, breeds in shallow water associated with meadows. Our generalized linear model (GLM) accurately predicted ~84% of true presence-absence data on a subset of data withheld for testing. The predicted environmental quality of each meadow was iteratively ‘boosted’ by the quality of neighbors within dispersal distance. We used this park-wide meadow connectivity network to estimate the relative influence of an individual Meadow’s ‘environmental quality’ versus its ‘network quality’ to predict: a) clusters of high quality breeding meadows potentially linked by dispersal, b) breeding meadows with high environmental quality that are isolated from other such meadows, c) breeding meadows with lower environmental quality where long-term persistence may critically depend on the network neighborhood, and d) breeding meadows with the biggest impact on park-wide breeding patterns. Combined with targeted data on dispersal, genetics, disease, and other potential stressors, these results can guide designation of core conservation areas for A. canorus in Yosemite National Park.

Social relationships and depression: ten-year follow-up from a nationally representative study.

PubMed

Teo, Alan R; Choi, Hwajung; Valenstein, Marcia

2013-01-01

Social network characteristics have long been associated with mental health, but their longitudinal impact on depression is less known. We determined whether quality of social relationships and social isolation predicts the development of depression. The sample consisted of a cohort of 4,642 American adults age 25-75 who completed surveys at baseline in 1995-1996 and at ten-year follow-up. Quality of relationships was assessed with non-overlapping scales of social support and social strain and a summary measure of relationship quality. Social isolation was measured by presence of a partner and reported frequency of social contact. The primary outcome was past year major depressive episode at ten-year follow-up. Multivariable logistic regression was conducted, adjusting for the presence of potential confounders. Risk of depression was significantly greater among those with baseline social strain (OR, 1.99; 95% CI, 1.47-2.70), lack of social support (OR, 1.79; 95% CI, 1.37-2.35), and poor overall relationship quality (OR 2.60; 95% CI, 1.84-3.69). Those with the lowest overall quality of social relationships had more than double the risk of depression (14.0%; 95% CI, 12.0-16.0; p<.001) than those with the highest quality (6.7%; 95% CI, 5.3-8.1; p<.001). Poor quality of relationship with spouse/partner and family each independently increased risk of depression. Social isolation did not predict future depression, nor did it moderate the effect of relationship quality. Quality of social relationships is a major risk factor for major depression. Depression interventions should consider targeting individuals with low quality of social relationships.

Social Relationships and Depression: Ten-Year Follow-Up from a Nationally Representative Study

PubMed Central

Teo, Alan R.; Choi, HwaJung; Valenstein, Marcia

2013-01-01

Background Social network characteristics have long been associated with mental health, but their longitudinal impact on depression is less known. We determined whether quality of social relationships and social isolation predicts the development of depression. Methods The sample consisted of a cohort of 4,642 American adults age 25–75 who completed surveys at baseline in 1995–1996 and at ten-year follow-up. Quality of relationships was assessed with non-overlapping scales of social support and social strain and a summary measure of relationship quality. Social isolation was measured by presence of a partner and reported frequency of social contact. The primary outcome was past year major depressive episode at ten-year follow-up. Multivariable logistic regression was conducted, adjusting for the presence of potential confounders. Results Risk of depression was significantly greater among those with baseline social strain (OR, 1.99; 95% CI, 1.47–2.70), lack of social support (OR, 1.79; 95% CI, 1.37–2.35), and poor overall relationship quality (OR 2.60; 95% CI, 1.84–3.69). Those with the lowest overall quality of social relationships had more than double the risk of depression (14.0%; 95% CI, 12.0–16.0; p<.001) than those with the highest quality (6.7%; 95% CI, 5.3–8.1; p<.001). Poor quality of relationship with spouse/partner and family each independently increased risk of depression. Social isolation did not predict future depression, nor did it moderate the effect of relationship quality. Conclusions Quality of social relationships is a major risk factor for major depression. Depression interventions should consider targeting individuals with low quality of social relationships. PMID:23646128

Fungi in spices and mycotoxigenic potential of some Aspergilli isolated.

PubMed

Garcia, Marcelo Valle; Parussolo, Gilson; Moro, Camila Brombilla; Bernardi, Angélica Olivier; Copetti, Marina Venturini

2018-08-01

The aim of this study was to identify fungal species present in 200 samples of rosemary, fennel, cinnamon, clove, pepperoni, black and white pepper and oregano and evaluate the mycotoxigenic potential of the some Aspergilli isolated. Clove, black and white peppers were analyzed by direct plating. For rosemary, cinnamon, fennel, pepperoni pepper and oregano samples were used spread plate. Mycotoxigenic capacity was verified by the agar plug method. With the exception of clove, all the spices showed high fungal contamination, especially by Aspergillus sp., Penicillium sp. and Cladosporium sp. Frequency of toxigenic Aspergillus spp. was intense in white and black peppers, with presence of Aspergillus flavus (up to 32%), Aspergillus nomius (up to 12%), Aspergillus parasiticus (up to 4%), Aspergillus niger complex (up to 52%), Aspergillus ochraceus (up 12%) and Aspergillus carbonarius (up to 4%). 14,2% of A. flavus isolated from black pepper were aflatoxins producers. In the white pepper, 66.7% of A. flavus isolates and 100% of A. nomius were aflatoxigenic. Oregano showed the highest number of A. niger complex isolates (49), however, only 2.04% produced ochratoxin A. This study showed a huge fungal presence in spices, which could compromise the sensorial quality of these products and represent a hazard for consumers. Copyright © 2018. Published by Elsevier Ltd.

Spherical quartz crystals investigated with synchrotron radiation

DOE PAGES

Pereira, N. R.; Macrander, A. T.; Hill, K. W.; ...

2015-10-27

The quality of x-ray spectra and images obtained from plasmas with spherically bent crystals depends in part on the crystal's x-ray diffraction across the entire crystal surface. We employ the energy selectivity and high intensity of synchrotron radiation to examine typical spherical crystals from alpha-quartz for their diffraction quality, in a perpendicular geometry that is particularly convenient to examine sagittal focusing. The crystal's local diffraction is not ideal: the most noticeable problems come from isolated regions that so far have failed to correlate with visible imperfections. In conclusion, excluding diffraction from such problem spots has little effect on the focusmore » beyond a decrease in background.« less

Evaluation of Bacillus spp. as dough starters for Adhirasam - A traditional rice based fermented food of Southern India

PubMed Central

Anisha, Anvar Hussain Noorul; Anandham, Rangasamy; Kwon, Soon Woo; Gandhi, Pandiyan Indira; Gopal, Nellaiappan Olaganathan

2015-01-01

Abstract Adhirasam is a cereal based, doughnut shaped, deep fried dessert consumed in the southern regions of India. The dough used to prepare adhirasam is fermented and contains rice flour and jaggery. The aim of the present study was to characterize the cultivable bacteria associated with this fermented dough and to identify a suitable starter culture for the production of quality adhirasam. In total, one hundred and seventy bacterial isolates were recovered from de Man Rogosa Sharp (MRS) agar, nutrient agar, lysogeny agar and tryptic soy agar media. Out of the 170 bacterial isolates, sixteen isolates were selected based on their ability to tolerate glucose and sucrose. All the bacterial isolates tolerated 15% glucose and 30% sucrose. Analyses of 16S rDNA gene sequences of the bacterial isolates showed that the dominant cultivable bacteria were members of the genus Bacillus. These strains were further used as starters and tested for their ability to ferment rice flour with jaggery to produce adhirasam dough. Organoleptic evaluation was carried out to choose the best starter strain. Adhirasam prepared from Bacillus subtilis isolates S4-P11, S2-G2-A1 and S1-G15, Bacillus tequilensis isolates S2-H16, S3-P9, S3-G10 and Bacillus siamensis isolate S2-G13 were highly acceptable to consumers. Adhirasam prepared using these starter cultures had superior product characteristics such as softness in texture, flavor and enhanced aroma and sweet taste. PMID:26691480

A new anthraquinone and eight constituents from Hedyotis caudatifolia Merr. et Metcalf: isolation, purification and structural identification.

PubMed

Luo, Peng; Su, Jiale; Zhu, Yilin; Wei, Jianhua; Wei, Wanxing; Pan, Weigao

2016-10-01

Hedyotis caudatifolia Merr. et Metcalf. (HC), a folk medicine in Yao nationalities areas in China, was used to investigate the chemical constituents. Through silica gel and Sephadex LH-20 column chromatography, nine compounds were isolated and purified. By physical and chemical properties, IR, MS (EI-MS, high resolution EI-MS), 1D NMR ((1)H NMR, (13)C NMR) and 2D NMR (HSQC, (1)H-(1)H COSY, HMBC), their structures were identified as β-sitosterol (1), stigmasterol (2), scopolin (3), 2-hydroxy-1,7,8-trimethoxyanthracene-9,10-dione (4), oleanolic acid (5), ursolic acid (6), methyl barbinervate (7), β-daucosterol (8) and p-Hydroxybenzoic acid (9). These compounds were isolated from HC for the first time, and 4 a new anthraquinone whose biological activities are worth to be investigated in future. These compounds may contribute to the HC's pharmacological effects on treating diseases, and may be used as candidates for control index in establishing the quality control standard of HC.

The Quasar Pairs Environment At z ∼ 0.5

NASA Astrophysics Data System (ADS)

Sandrinelli, Angela; Falomo, R.; Treves, A.; Scarpa, R.; Uslenghi, M.

2016-10-01

We analyze the environment of a sample of 20 quasar physical pairs at 0.4

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

PubMed Central

Jeffares, Daniel C.; Jolly, Clemency; Hoti, Mimoza; Speed, Doug; Shaw, Liam; Rallis, Charalampos; Balloux, Francois; Dessimoz, Christophe; Bähler, Jürg; Sedlazeck, Fritz J.

2017-01-01

Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic diversity and evolution. We analyse the effects of SVs on gene expression, quantitative traits and intrinsic reproductive isolation in the yeast Schizosaccharomyces pombe. We establish a high-quality curated catalogue of SVs in the genomes of a worldwide library of S. pombe strains, including duplications, deletions, inversions and translocations. We show that copy number variants (CNVs) show a variety of genetic signals consistent with rapid turnover. These transient CNVs produce stoichiometric effects on gene expression both within and outside the duplicated regions. CNVs make substantial contributions to quantitative traits, most notably intracellular amino acid concentrations, growth under stress and sugar utilization in winemaking, whereas rearrangements are strongly associated with reproductive isolation. Collectively, these findings have broad implications for evolution and for our understanding of quantitative traits including complex human diseases. PMID:28117401

Hofmeister series salts enhance purification of plasmid DNA by non-ionic detergents

PubMed Central

Lezin, George; Kuehn, Michael R.; Brunelli, Luca

2011-01-01

Ion-exchange chromatography is the standard technique used for plasmid DNA purification, an essential molecular biology procedure. Non-ionic detergents (NIDs) have been used for plasmid DNA purification, but it is unclear whether Hofmeister series salts (HSS) change the solubility and phase separation properties of specific NIDs, enhancing plasmid DNA purification. After scaling-up NID-mediated plasmid DNA isolation, we established that NIDs in HSS solutions minimize plasmid DNA contamination with protein. In addition, large-scale NID/HSS solutions eliminated LPS contamination of plasmid DNA more effectively than Qiagen ion-exchange columns. Large-scale NID isolation/NID purification generated increased yields of high quality DNA compared to alkali isolation/column purification. This work characterizes how HSS enhance NID-mediated plasmid DNA purification, and demonstrates that NID phase transition is not necessary for LPS removal from plasmid DNA. Specific NIDs such as IGEPAL CA-520 can be utilized for rapid, inexpensive and efficient laboratory-based large-scale plasmid DNA purification, outperforming Qiagen-based column procedures. PMID:21351074

mirRICH, a simple method to enrich the small RNA fraction from over-dried RNA pellets.

PubMed

Choi, Cheolwon; Yoon, Seulgi; Moon, Hyesu; Bae, Yun-Ui; Kim, Chae-Bin; Diskul-Na-Ayudthaya, Penchatr; Ngu, Trinh Van; Munir, Javaria; Han, JaeWook; Park, Se Bin; Moon, Jong-Seok; Song, Sujung; Ryu, Seongho

2018-04-11

Techniques to isolate the small RNA fraction (<200nt) by column-based methods are commercially available. However, their use is limited because of the relatively high cost. We found that large RNA molecules, including mRNAs and rRNAs, are aggregated together in the presence of salts when RNA pellets are over-dried. Moreover, once RNA pellets are over-dried, large RNA molecules are barely soluble again during the elution process, whereas small RNA molecules (<100nt) can be eluted. We therefore modified the acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA extraction protocol by skipping the 70% ethanol washing step and over-drying the RNA pellet for 1 hour at room temperature. We named this novel small RNA isolation method "mirRICH." The quality of the small RNA sequences was validated by electrophoresis, next-generation sequencing, and quantitative PCR, and the findings support that our newly developed column-free method can successfully and efficiently isolate small RNAs from over-dried RNA pellets.

The power in being together for young adults who have heart disease - the photoshoot experience.

PubMed

Gallagher, Robyn; Potter, Ellen; Thomson Mangnall, Linda; Ladak, Laila; Gallagher, Patrick; Neubeck, Lis

The study aimed to determine perceived motivations and benefits of photoshoot participation for young adults who have heart disease. Feeling isolated and different can have lifelong affects on quality of life in heart disease survivors. Photoshoots, where people create a photographic image of themselves, promote positive interpretation of their cardiac illness experience, but participant experiences remain under-investigated. Young adult heart disease support group members completing a photoshoot were interviewed and data were thematically analyzed. Seven females and one male aged 20-47 years participated. The main theme, People Like Me, emphasized feelings of being different, isolated and uncertain due to the heart disease. Other themes related to support gained from people who were not like them, gaining and providing support to their peers. The photoshoot enabled a highly valued collective feeling. For young adult heart disease survivors, the photoshoot provides a fun, social opportunity to reduce isolation and share experiences. Copyright © 2017 Elsevier Inc. All rights reserved.

Pyrosequencing as a tool for the identification of common isolates of Mycobacterium sp.

PubMed

Tuohy, Marion J; Hall, Gerri S; Sholtis, Mary; Procop, Gary W

2005-04-01

Pyrosequencing technology, sequencing by addition, was evaluated for categorization of mycobacterial isolates. One hundred and eighty-nine isolates, including 18 ATCC and Trudeau Mycobacterial Culture Collection (TMC) strains, were studied. There were 38 Mycobacterium tuberculosis complex, 27 M. kansasii, 27 MAI complex, 21 M. marinum, 14 M. gordonae, 20 M. chelonae-abscessus group, 10 M. fortuitum, 5 M. xenopi, 3 M. celatum, 2 M. terrae complex, 20 M. mucogenicum, and 2 M. scrofulaceum. Nucleic acid extracts were prepared from solid media or MGIT broth. Traditional PCR was performed with one of the primers biotinylated; the assay targeted a portion of the 16S rRNA gene that contains a hypervariable region, which has been previously shown to be useful for the identification of mycobacteria. The PSQ Sample Preparation Kit was used, and the biotinylated PCR product was processed to a single-stranded DNA template. The sequencing primer was hybridized to the DNA template in a PSQ96 plate. Incorporation of the complementary nucleotides resulted in light generation peaks, forming a pyrogram, which was evaluated by the instrument software. Thirty basepairs were used for isolate categorization. Manual interpretation of the sequences was performed if the quality of the 30-bp sequence was in doubt or if more than 4 bp homopolymers were recognized. Sequences with more than 5 bp of bad quality were deemed unacceptable. When blasted against GenBank, 179 of 189 sequences (94.7%) assigned isolates to the correct molecular genus or group. Ten M. gordonae isolates had more than 5 bp of bad quality sequence and were not accepted. Pyrosequencing of this hypervariable region afforded rapid and acceptable characterization of common, routinely isolated clinical Mycobacterium sp. Algorithms are recommended for further differentiation with an additional sequencing primer or additional biochemicals.

Quality of life and social isolation in Greek adolescents with primary focal hyperhidrosis treated with botulinum toxin type A: a case series.

PubMed

Kouris, Anargyros; Armyra, Kalliopi; Stefanaki, Christina; Christodoulou, Christos; Karimali, Polixeni; Kontochristopoulos, George

2015-01-01

Primary hyperhidrosis, although extensively documented in adults, typically has onset that dates back to early childhood. It is an unpleasant and socially disabling problem for the affected child, but little attention has been paid to the disease in adolescents. The objective of the current study was to evaluate the effectiveness of botulinum toxin type A (BTXA) in adolescents with primary palmar and axillary hyperhidrosis and to determine its effect on quality of life and social isolation. Thirty-five individuals (17 girls, 18 boys) with moderate to severe palmar and axillary hyperhidrosis were treated with BTXA (onabotulinum). Patients were examined at baseline and 6 months after treatment. The Hyperhidrosis Disease Severity Scale (HDSS) was used to evaluate disease severity and the Children's Dermatology Life Quality Index (CDLQI) was used to assess quality of life. The University of California at Los Angeles loneliness scale (UCLA version 3) was used to assess personal perception of loneliness and social isolation. The median age of the participants was 14 years, and 48.6% were female. Twenty-one had palmar hyperhidrosis, and 14 had axillary hyperhidrosis. Total CDLQI and social isolation scores decreased significantly after treatment with BTXA (both p < 0.001). There was a significant difference between pre- and post-treatment levels of severity of hyperhidrosis. No statistically significant difference was documented for CDLQI and UCLA scores between boys and girls. Treatment of hyperhidrosis with BTXA resulted in improvement in quality of life, social skills, and activities. © 2014 Wiley Periodicals, Inc.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

PubMed Central

Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.; Hugenholtz, Philip; Tyson, Gene W.

2015-01-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. PMID:25977477

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

PubMed

Parks, Donovan H; Imelfort, Michael; Skennerton, Connor T; Hugenholtz, Philip; Tyson, Gene W

2015-07-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. © 2015 Parks et al.; Published by Cold Spring Harbor Laboratory Press.

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

PubMed Central

Elekwachi, Chijioke O.; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J.

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa. PMID:28983291

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.

PubMed

Elekwachi, Chijioke O; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa.

Effect of Habitat Size, Quality, and Isolation on Functional Groups of Beetles in Hollow Oaks

PubMed Central

Pilskog, Hanne Eik; Birkemoe, Tone; Framstad, Erik; Sverdrup-Thygeson, Anne

2016-01-01

One of the largest threats to biodiversity is land use change and habitat loss. Hollow oaks (Quercus spp. L.) are well-defined patches that are hotspots for biodiversity and red-listed species, but they are often rare and fragmented in the landscape. We investigated the effect of patch size, habitat quality, and isolation on functional groups and red-listed saproxylic beetles in hollow oaks (n = 40) in Norway. The groups were defined by host tree association, trophic grouping, and red-listed status. Habitat quality, represented by tree form was most important in explaining species richness for most groups. Patch size, represented by circumference and amount of dead branches, was most important in explaining abundance. Isolation, that is single oaks compared with oaks in groups, had a negative effect on the abundance of beetles feeding both on wood and fungi (xylomycethopagous), as well as on species associated with broadleaved trees (oak semi-specialists), but did not affect species richness. This indicates that at this scale and in this landscape, isolated oaks are as species rich and valuable for conservation as other oaks, although some functional groups may be more vulnerable to isolation than others. The red-listed species only responded to patch size, indicating that oaks with large circumference and many dead branches are especially important for red-listed species and for conservation. PMID:26945089

Characterization of Extracellular Vesicles by Size-Exclusion High-Performance Liquid Chromatography (HPLC).

PubMed

Huang, Tao; He, Jiang

2017-01-01

Extracellular vesicles (EVs) have recently attracted substantial attention due to the potential diagnostic and therapeutic relevance. Although a variety of techniques have been used to isolate and analyze EVs, it is still far away from satisfaction. Size-exclusion chromatography (SEC), which separates subjects by size, has been widely applied in protein purification and analysis. The purpose of this chapter is to show the applications of size-exclusion high-performance liquid chromatography (HPLC) as methods for EV characterization of impurities or contaminants of small size, and thus for quality assay for the purity of the samples of EVs.

Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study of Rhodobacter sp., Isolated from High Altitude Wetlands in Chile

PubMed Central

Pérez, Vilma; Hengst, Martha; Kurte, Lenka; Dorador, Cristina; Jeffrey, Wade H.; Wattiez, Ruddy; Molina, Veronica; Matallana-Surget, Sabine

2017-01-01

Salar de Huasco, defined as a polyextreme environment, is a high altitude saline wetland in the Chilean Altiplano (3800 m.a.s.l.), permanently exposed to the highest solar radiation doses registered in the world. We present here the first comparative proteomics study of a photoheterotrophic bacterium, Rhodobacter sp., isolated from this remote and hostile habitat. We developed an innovative experimental approach using different sources of radiation (in situ sunlight and UVB lamps), cut-off filters (Mylar, Lee filters) and a high-throughput, label-free quantitative proteomics method to comprehensively analyze the effect of seven spectral bands on protein regulation. A hierarchical cluster analysis of 40 common proteins revealed that all conditions containing the most damaging UVB radiation induced similar pattern of protein regulation compared with UVA and visible light spectral bands. Moreover, it appeared that the cellular adaptation of Rhodobacter sp. to osmotic stress encountered in the hypersaline environment from which it was originally isolated, might further a higher resistance to damaging UV radiation. Indeed, proteins involved in the synthesis and transport of key osmoprotectants, such as glycine betaine and inositol, were found in very high abundance under UV radiation compared to the dark control, suggesting the function of osmolytes as efficient reactive oxygen scavengers. Our study also revealed a RecA-independent response and a tightly regulated network of protein quality control involving proteases and chaperones to selectively degrade misfolded and/or damaged proteins. PMID:28694800

Isolation and properties of cellulose nanofibrils from coconut palm petioles by different mechanical process.

PubMed

Xu, Changyan; Zhu, Sailing; Xing, Cheng; Li, Dagang; Zhu, Nanfeng; Zhou, Handong

2015-01-01

In this study, cellulose nanofibrils (CNFs) were successfully isolated from coconut palm petiole residues falling off naturally with chemical pretreatments and mechanical treatments by a grinder and a homogenizor. FTIR spectra analysis showed that most of hemicellulose and lignin were removed from the fiber after chemical pretreatments. The compositions of CNFS indicated that high purity of nanofibrils with cellulose contain more than 95% was obtained. X-ray diffractogram demonstrated that chemical pretreatments significantly increased the crystallinity of CNFs from 38.00% to 70.36%; however, 10-15 times of grinding operation followed by homogenizing treatment after the chemical pretreatments did not significantly improve the crystallinity of CNFs. On the contrary, further grinding operation could destroy crystalline regions of the cellulose. SEM image indicated that high quality of CNFs could be isolated from coconut palm petiole residues with chemical treatments in combination of 15 times of grinding followed by 10 times of homogenization and the aspect ratio of the obtained CNFs ranged from 320 to 640. The result of TGA-DTG revealed that the chemical-mechanical treatments improved thermal stability of fiber samples, and the CNFs with 15 grinding passing times had the best thermal stability. This work suggests that the CNFs can be successfully extracted from coconut palm petiole residues and it may be a potential feedstock for nanofiber reinforced composites due to its high aspect ratio and crystallinity.

Isolation and Properties of Cellulose Nanofibrils from Coconut Palm Petioles by Different Mechanical Process

PubMed Central

Li, Dagang; Zhu, Nanfeng

2015-01-01

In this study, cellulose nanofibrils (CNFs) were successfully isolated from coconut palm petiole residues falling off naturally with chemical pretreatments and mechanical treatments by a grinder and a homogenizor. FTIR spectra analysis showed that most of hemicellulose and lignin were removed from the fiber after chemical pretreatments. The compositions of CNFS indicated that high purity of nanofibrils with cellulose contain more than 95% was obtained. X-ray diffractogram demonstrated that chemical pretreatments significantly increased the crystallinity of CNFs from 38.00% to 70.36%; however, 10-15 times of grinding operation followed by homogenizing treatment after the chemical pretreatments did not significantly improve the crystallinity of CNFs. On the contrary, further grinding operation could destroy crystalline regions of the cellulose. SEM image indicated that high quality of CNFs could be isolated from coconut palm petiole residues with chemical treatments in combination of 15 times of grinding followed by 10 times of homogenization and the aspect ratio of the obtained CNFs ranged from 320 to 640. The result of TGA-DTG revealed that the chemical-mechanical treatments improved thermal stability of fiber samples, and the CNFs with 15 grinding passing times had the best thermal stability. This work suggests that the CNFs can be successfully extracted from coconut palm petiole residues and it may be a potential feedstock for nanofiber reinforced composites due to its high aspect ratio and crystallinity. PMID:25875280

Methicillin-resistant Staphylococcus aureus in HIV patients: risk factors associated with colonization and/or infection and methods for characterization of isolates - a systematic review.

PubMed

Ferreira, Dennis de Carvalho; Silva, Glaucilene Rodrigues da; Cavalcante, Fernanda Sampaio; Carmo, Flavia Lima do; Fernandes, Leonardo Alexandre; Moreira, Suelen; Passos, Mauro Romero Leal; Colombo, Ana Paula Vieira; Santos, Katia Regina Netto dos

2014-11-01

Staphylococcus aureus is an important cause of infections and HIV-infected individuals are frequently susceptible to this pathogen. The aim of this study was to perform a systematic review to identify both the risk factors associated with colonization/infection by methicillin-resistant S. aureus in HIV patients and the methods used for characterization of isolates. An electronic search of articles published between January 2001 and December 2013 was first conducted. Among 116 studies categorized as being at a quality level of A, B or C, only 9 studies were considered to have high methodological quality (level A). The majority of these studies were retrospective (4/9 studies). The risk factors associated with colonization/infection by S. aureus were use of antimicrobials (4/9 studies), previous hospitalization (4/9 studies) and low CD4+ T lymphocyte counts (<200 cells/μl) (3/9 studies). Culture in mannitol salt agar (3/9 studies) and the latex agglutination test (5/9 studies) were the main methods used for bacterial phenotypic identification. Genotypic profiles were accessed by pulsed-field gel electrophoresis (6/9 studies) and USA300 was the most prevalent lineage (5/9 studies). Most isolates were resistant to erythromycin (3/9 studies) and susceptible to vancomycin (4/9 studies). Ultimately, use of antimicrobials and previous hospitalization were the main risk factors for colonization/infection by methicillin-resistant S. aureus in HIV-infected individuals. However, the numbers of evaluated patients, the exclusion and inclusion criteria and the characterization of the S. aureus isolates were not uniform, which made it difficult to establish the characteristics associated with HIV patients who are colonized/infected by S. aureus.

Successes and Short Comings in Four Years of an International External Quality Assurance Program for Animal Influenza Surveillance

PubMed Central

Spackman, Erica; Cardona, Carol; Muñoz-Aguayo, Jeannette; Fleming, Susan

2016-01-01

The US National institutes of Health-Centers of Excellence for Influenza Research and Surveillance is a research consortium that funds numerous labs worldwide to conduct influenza A surveillance in diverse animal species. There is no harmonization of testing procedures among these labs; therefore an external quality assurance (EQA) program was implemented to evaluate testing accuracy among labs in the program in 2012. Accurate detection of novel influenza A variants is crucial because of the broad host range and potentially high virulence of the virus in diverse species. Two molecular detection sample sets and 2 serology sample sets (one with avian origin isolates, and one with mammalian origin isolates each) were made available at approximately six month intervals. Participating labs tested the material in accordance with their own protocols. During a five year period a total of 41 labs from 23 countries ordered a total of 132 avian molecular, 121 mammalian molecular and 90 serology sample sets. Testing was completed by 111 individuals. Detection of type A influenza by RT-PCR was reliable with a pass rate (80% or greater agreement with expected results) of 86.6% for avian and 86.2% for mammalian origin isolates. However, identification of subtype by RT-PCR was relatively poor with 54.1% and 75.9% accuracy for avian and mammalian influenza isolates respectively. Serological testing had an overall pass rate of 86.9% and 22/23 labs used commercial ELISA kits. Based on the results of this EQA program six labs modified their procedures to improve accuracy and one lab identified an unknown equipment problem. These data represent the successful implementation of an international EQA program for an infectious disease; insights into the logistics and test design are also discussed. PMID:27788155

Successes and Short Comings in Four Years of an International External Quality Assurance Program for Animal Influenza Surveillance.

PubMed

Spackman, Erica; Cardona, Carol; Muñoz-Aguayo, Jeannette; Fleming, Susan

2016-01-01

The US National institutes of Health-Centers of Excellence for Influenza Research and Surveillance is a research consortium that funds numerous labs worldwide to conduct influenza A surveillance in diverse animal species. There is no harmonization of testing procedures among these labs; therefore an external quality assurance (EQA) program was implemented to evaluate testing accuracy among labs in the program in 2012. Accurate detection of novel influenza A variants is crucial because of the broad host range and potentially high virulence of the virus in diverse species. Two molecular detection sample sets and 2 serology sample sets (one with avian origin isolates, and one with mammalian origin isolates each) were made available at approximately six month intervals. Participating labs tested the material in accordance with their own protocols. During a five year period a total of 41 labs from 23 countries ordered a total of 132 avian molecular, 121 mammalian molecular and 90 serology sample sets. Testing was completed by 111 individuals. Detection of type A influenza by RT-PCR was reliable with a pass rate (80% or greater agreement with expected results) of 86.6% for avian and 86.2% for mammalian origin isolates. However, identification of subtype by RT-PCR was relatively poor with 54.1% and 75.9% accuracy for avian and mammalian influenza isolates respectively. Serological testing had an overall pass rate of 86.9% and 22/23 labs used commercial ELISA kits. Based on the results of this EQA program six labs modified their procedures to improve accuracy and one lab identified an unknown equipment problem. These data represent the successful implementation of an international EQA program for an infectious disease; insights into the logistics and test design are also discussed.

Microaspiration of Solanum tuberosum root cells at early stages of infection by Globodera pallida.

PubMed

Kooliyottil, Rinu; Dandurand, Louise-Marie; Kuhl, Joseph C; Caplan, Allan; Xiao, Fangming

2017-01-01

Sedentary endoparasitic cyst nematodes form a feeding structure in plant roots, called a syncytium. Syncytium formation involves extensive transcriptional modifications, which leads to cell modifications such as increased cytoplasmic streaming, enlarged nuclei, increased numbers of organelles, and replacement of a central vacuole by many small vacuoles. When whole root RNA is isolated and analyzed, transcript changes manifested in the infected plant cells are overshadowed by gene expression from cells of the entire root system. Use of microaspiration allows isolation of the content of nematode infected cells from a heterogeneous cell population. However, one challenge with this method is identifying the nematode infected cells under the microscope at early stages of infection. This problem was addressed by staining nematode juveniles with a fluorescent dye prior to infection so that the infected cells could be located and microaspirated. In the present study, we used the fluorescent vital stain PKH26 coupled with a micro-rhizosphere chamber to locate the infected nematode Globodera pallida in Solanum tuberosum root cells. This enabled microaspiration of nematode-infected root cells during the early stages of parasitism. To study the transcriptional events occurring in these cells, an RNA isolation method from microaspirated samples was optimized, and subsequently the RNA was purified using magnetic beads. With this method, we obtained an RNA quality number of 7.8. For transcriptome studies, cDNA was synthesized from the isolated RNA and assessed by successfully amplifying several pathogenesis related protein coding genes. The use of PKH26 stained nematode juveniles enabled early detection of nematode infected cells for microaspiration. To investigate transcriptional changes in low yielding RNA samples, bead-based RNA extraction procedures minimized RNA degradation and provided high quality RNA. This protocol provides a robust procedure to analyze gene expression in nematode-infected cells.

Benthic cyanobacteria: A source of cylindrospermopsin and microcystin in Australian drinking water reservoirs.

PubMed

Gaget, Virginie; Humpage, Andrew R; Huang, Qiong; Monis, Paul; Brookes, Justin D

2017-11-01

Cyanobacteria represent a health hazard worldwide due to their production of a range of highly potent toxins in diverse aquatic environments. While planktonic species have been the subject of many investigations in terms of risk assessment, little is known about benthic forms and their impact on water quality or human and animal health. This study aimed to purify isolates from environmental benthic biofilms sampled from three different drinking water reservoirs and to assess their toxin production by using the following methods: Enzyme-Linked Immunosorbent Assay (ELISA), High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and quantitative PCR (qPCR). Microscopic observation of the isolates allowed the identification of various filamentous cyanobacterial genera: Anabaena (benthic form), Calothrix and Nostoc from the Nostocales and Geitlerinema, Leptolyngbya, Limnothrix, Lyngbya, Oxynema, Phormidium and Pseudanabaena representing non-heterocystous filamentous cyanobacteria. The Phormidium ambiguum strain AWQC-PHO021 was found to produce 739 ng/mg of dry weight (d/w) of cylindrospermopsin and 107 ng/mg (d/w) of deoxy-cylindrospermopsin. The Nostoc linckia strain AWQC-NOS001 produced 400 ng/mg (d/w) of a microcystin analogue. This is the first report of hepatotoxin production by benthic cyanobacteria in temperate Australian drinking water reservoirs. These findings indicate that water quality monitoring programs need to consider benthic cyanobacteria as a potential source of toxins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient isolation method for high-quality genomic DNA from cicada exuviae.

PubMed

Nguyen, Hoa Quynh; Kim, Ye Inn; Borzée, Amaël; Jang, Yikweon

2017-10-01

In recent years, animal ethics issues have led researchers to explore nondestructive methods to access materials for genetic studies. Cicada exuviae are among those materials because they are cast skins that individuals left after molt and are easily collected. In this study, we aim to identify the most efficient extraction method to obtain high quantity and quality of DNA from cicada exuviae. We compared relative DNA yield and purity of six extraction protocols, including both manual protocols and available commercial kits, extracting from four different exoskeleton parts. Furthermore, amplification and sequencing of genomic DNA were evaluated in terms of availability of sequencing sequence at the expected genomic size. Both the choice of protocol and exuvia part significantly affected DNA yield and purity. Only samples that were extracted using the PowerSoil DNA Isolation kit generated gel bands of expected size as well as successful sequencing results. The failed attempts to extract DNA using other protocols could be partially explained by a low DNA yield from cicada exuviae and partly by contamination with humic acids that exist in the soil where cicada nymphs reside before emergence, as shown by spectroscopic measurements. Genomic DNA extracted from cicada exuviae could provide valuable information for species identification, allowing the investigation of genetic diversity across consecutive broods, or spatiotemporal variation among various populations. Consequently, we hope to provide a simple method to acquire pure genomic DNA applicable for multiple research purposes.

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

DOE PAGES

Ardley, Julie; Tian, Rui; O’Hara, Graham; ...

2015-12-01

We report that Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.)more » Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ardley, Julie; Tian, Rui; O’Hara, Graham

We report that Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.)more » Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

Mycoflora and mycotoxins in Brazilian black pepper, white pepper and Brazil nuts.

PubMed

Freire, F C; Kozakiewicz, Z; Paterson, R R

2000-01-01

A wide range of field and storage fungi were isolated from black pepper, white pepper and Brazil nut kernels from Amazonia. A total of 42 species were isolated from both peppers. Aspergillus flavus and A. niger were isolated more frequently from black than from white pepper. Other potential mycotoxigenic species isolated included: A. ochraceus, A. tamarii, A. versicolor, Emericella nidulans and Chaetomium globosum, Penicillium brevicompactum, P. citrinum, P. islandicum and P. glabrum. Species isolated from pepper for the first time were Acrogenospora sphaerocephala, Cylindrocarpon lichenicola, Lacellinopsis sacchari, Microascus cinereus, Petriella setifera and Sporormiella minima. Seventeen species were isolated from Brazil nut kernels. A. flavus was the dominant species followed by A. niger. P. citrinum and P. glabrum were the only penicillia isolated. Species isolated for the first time included Acremonium curvulum, Cunninghamella elegans, Exophiala sp., Fusarium oxysporum, Pseudoallescheria boydii, Rhizopus oryzae, Scopulariopsis sp., Thielavia terricola and Trichoderma citrinoviride. Considerably more metabolites were detected from black than white pepper in qualitative analyses. Chaetocin, penitrem A, and xanthocillin were identified only from black pepper, and tenuazonic acid was identified from both black and white pepper. Aflatoxin G2, chaetoglobosin C, and spinulosin were identified from poor quality brazil nuts. Aflatoxin B1 and B2 were also only detected in poor quality brazil nuts at concentrations of 27.1 micrograms kg-1 and 2.1 micrograms kg-1 respectively (total 29.2 micrograms kg-1).

[Current aspects of the definition and diagnosis of sepsis and antibiotic resistance].

PubMed

Brunkhorst, Frank M; Gastmeier, Petra; Abu Sin, Muna

2018-05-01

Hospital mortality of patients with secondary sepsis remains high at around 40%. Because of the methodological deficiencies of the definitions used so far, valid epidemiological data on secondary sepsis that allow for national and international comparisons are lacking. Since 2016, new clinical diagnostic tools that are also suitable for sepsis screening outside of intensive care units have been available. To counteract the high mortality of nosocomial sepsis, new approaches to the early identification of at-risk patients are needed. An adequate blood culture sampling rate and a high preanalytical quality should be established as a basis for quality assurance, especially in the field of nosocomial bloodstream infections; otherwise, there is a risk of surveillance bias. Data from laboratory-based antibiotic resistance surveillance on MRSA in blood culture isolates have shown a downward trend over the last 4 years. In Gram-negative pathogens, a relatively stable resistance situation has been observed over this period for many of the pathogen-antibiotic combinations.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.

PubMed

Zhang, Qiang; Wang, Tingting; Zhou, Qian; Zhang, Peng; Gong, Yanhai; Gou, Honglei; Xu, Jian; Ma, Bo

2017-01-23

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms

PubMed Central

Zhang, Qiang; Wang, Tingting; Zhou, Qian; Zhang, Peng; Gong, Yanhai; Gou, Honglei; Xu, Jian; Ma, Bo

2017-01-01

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches. PMID:28112223

Experimental equipment for an advanced ISOL facility[Isotope Separation On-Line Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baktash, C.; Lee, I.Y.; Rehm, K.E.

This report summarizes the proceedings and recommendations of the Workshop on the Experimental Equipment for an Advanced ISOL Facility which was held at Lawrence Berkeley National Laboratory on July 22--25, 1998. The purpose of this workshop was to discuss the performance requirements, manpower and cost estimates, as well as a schedule of the experimental equipment needed to fully exploit the new physics which can be studied at an advanced ISOL facility. An overview of the new physics opportunities that would be provided by such a facility has been presented in the White Paper that was issued following the Columbus Meeting.more » The reactions and experimental techniques discussed in the Columbus White Paper served as a guideline for the formulation of the detector needs at the Berkeley Workshop. As outlined a new ISOL facility with intense, high-quality beams of radioactive nuclei would provide exciting new research opportunities in the areas of: the nature of nucleonic matter; the origin of the elements; and tests of the Standard Model. After an introductory section, the following equipment is discussed: gamma-ray detectors; recoil separators; magnetic spectrographs; particle detectors; targets; and apparatus using non-accelerated beams.« less

Development of a novel automated cell isolation, expansion, and characterization platform.

PubMed

Franscini, Nicola; Wuertz, Karin; Patocchi-Tenzer, Isabel; Durner, Roland; Boos, Norbert; Graf-Hausner, Ursula

2011-06-01

Implementation of regenerative medicine in the clinical setting requires not only biological inventions, but also the development of reproducible and safe method for cell isolation and expansion. As the currently used manual techniques do not fulfill these requirements, there is a clear need to develop an adequate robotic platform for automated, large-scale production of cells or cell-based products. Here, we demonstrate an automated liquid-handling cell-culture platform that can be used to isolate, expand, and characterize human primary cells (e.g., from intervertebral disc tissue) with results that are comparable to the manual procedure. Specifically, no differences could be observed for cell yield, viability, aggregation rate, growth rate, and phenotype. Importantly, all steps-from the enzymatic isolation of cells through the biopsy to the final quality control-can be performed completely by the automated system because of novel tools that were incorporated into the platform. This automated cell-culture platform can therefore replace entirely manual processes in areas that require high throughput while maintaining stability and safety, such as clinical or industrial settings. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

Social networks and links to isolation and loneliness among elderly HCBS clients.

PubMed

Medvene, Louis J; Nilsen, Kari M; Smith, Rachel; Ofei-Dodoo, Samuel; DiLollo, Anthony; Webster, Noah; Graham, Annette; Nance, Anita

2016-01-01

The purpose of this study was to explore the network types of HCBS clients based on the structural characteristics of their social networks. We also examined how the network types were associated with social isolation, relationship quality and loneliness. Forty personal interviews were carried out with HCBS clients to assess the structure of their social networks as indicated by frequency of contact with children, friends, family and participation in religious and community organizations. Hierarchical cluster analysis was conducted to identify network types. Four network types were found including: family (n = 16), diverse (n = 8), restricted (n = 8) and religious (n = 7). Family members comprised almost half of participants' social networks, and friends comprised less than one-third. Clients embedded in family, diverse and religious networks had significantly more positive relationships than clients embedded in restricted networks. Clients embedded in restricted networks had significantly higher social isolation scores and were lonelier than clients in diverse and family networks. The findings suggest that HCBS clients' isolation and loneliness are linked to the types of social networks in which they are embedded. The findings also suggest that clients embedded in restricted networks are at high risk for negative outcomes.

Global patterns of fragmentation and connectivity of mammalian carnivore habitat.

PubMed

Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; Rondinini, Carlo; Boitani, Luigi

2011-09-27

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation.

Global patterns of fragmentation and connectivity of mammalian carnivore habitat

PubMed Central

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; Rondinini, Carlo; Boitani, Luigi

2011-01-01

Although mammalian carnivores are vulnerable to habitat fragmentation and require landscape connectivity, their global patterns of fragmentation and connectivity have not been examined. We use recently developed high-resolution habitat suitability models to conduct comparative analyses and to identify global hotspots of fragmentation and connectivity for the world's terrestrial carnivores. Species with less fragmentation (i.e. more interior high-quality habitat) had larger geographical ranges, a greater proportion of habitat within their range, greater habitat connectivity and a lower risk of extinction. Species with higher connectivity (i.e. less habitat isolation) also had a greater proportion of high-quality habitat, but had smaller, not larger, ranges, probably reflecting shorter distances between habitat patches for species with restricted distributions; such species were also more threatened, as would be expected given the negative relationship between range size and extinction risk. Fragmentation and connectivity did not differ among Carnivora families, and body mass was associated with connectivity but not fragmentation. On average, only 54.3 per cent of a species' geographical range comprised high-quality habitat, and more troubling, only 5.2 per cent of the range comprised such habitat within protected areas. Identification of global hotspots of fragmentation and connectivity will help guide strategic priorities for carnivore conservation. PMID:21844043

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

DOE PAGES

Mazur, Andrzej; De Meyer, Sofie E.; Tian, Rui; ...

2015-07-16

We report that Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75more » RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Aquatic indicator bacteria in the high alpine zone.

PubMed

Stuart, S A; McFeters, G A; Schillinger, J E; Stuart, D G

1976-02-01

Selected waters from the high alpine zone within Grand Teton National Park, Wyoming, were analyzed for populations of indicator bacteria during the past three summers to determine the influence of various factors on the quality of these waters. In general the water quality was not significantly influenced by the presence or absence of human visitors but rather by the nature of the biological community through which the streams flowed. A minority of the coliforms that were recovered from all of the sites proved to be fecal coliforms. The fecal streptococci isolated were identified as the species that were found primarily in the fecal material of the native rodent and moose populations. It is concluded that management questions that relate to the carrying capacity of alpine areas should be approached with the aid of other biological parameters along with levels of indicator bacteria in the streams.

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazur, Andrzej; De Meyer, Sofie E.; Tian, Rui

We report that Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75more » RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Experimentally Isolating the Contributions of a Disturbed Ephemeral Drainage to a Headwater Stream in the Southern Appalachians

NASA Astrophysics Data System (ADS)

Gannon, J. P.; Lord, M.; Kinner, D. A.

2015-12-01

A growing body of evidence suggests contributions to runoff from ephemeral channels during events can exhibit significant control over water quality in higher order streams. Furthermore, field observations from a steep Appalachian catchment influenced by human activity suggest these disturbed ephemeral drainages exhibit significant control over turbidity, water temperature, and conductivity levels downstream. High turbidity during stormflow is a water quality problem in many areas of the Southern Appalachians. However, upland ephemeral channels are not included in the jurisdiction of the Clean Water Act. This offers little recourse if their contributions degrade the water quality of larger-scale streams and highlights the need for robust evidence of the potential impacts of ephemeral drainages. The aim of this research is to isolate the contribution of a disturbed ephemeral drainage by diverting its flow from the study stream network. Spatially and temporally distributed stream water samples taken during storms, when the channel is diverted or allowed to flow normally, will allow us to assess its contribution. In this poster, we present initial spatial and temporal streamwater chemistry and turbidity data as well as a detailed description of the stream network, study design, and diversion construction. We anticipate the findings of this study will be relevant to describing the environmental impact of disturbed ephemeral channels and to describing their potential influence on other water chemistry parameters downstream.

Applications of the silicon wafer direct-bonding technique to electron devices

NASA Astrophysics Data System (ADS)

Furukawa, K.; Nakagawa, A.

1990-01-01

A silicon wafer direct-bonding (SDB) technique has been developed. A pair of bare silicon wafers, as well as an oxidized wafer pair, are bonded throughout the wafer surfaces without any bonding material. Conventional semiconductor device processes can be used for the bonded wafers, since the bonded interface is stable thermally, chemically, mechanically and electrically. Therefore, the SDB technique is very attractive, and has been applied to several kinds of electron devices. Bare silicon to bare silicon bonding is an alternative for epitaxial growth. A thick, high quality and high resistivity layer on a low resistivity substrate was obtained without autodoping. 1800 V insulated gate bipolar transistors were developed using these SDB wafers. No electrical resistance was observed at the bonded bare silicon interfaces. If oxidized wafers are bonded, the two wafers are electrically isolated, providing silicon on insulator (SOI) wafers. Dielectrically isolated photodiode arrays were fabricated on the SOI wafers and 500 V power IC's are now being developed.

Sicklepod (Senna obtusifolia) seed processing and potential utilization.

PubMed

Harry-O'kuru, Rogers E; Wu, Y Victor; Evangelista, Roque; Vaughn, Steven F; Rayford, Warren; Wilson, Richard F

2005-06-15

Sicklepod (Senna obtusifolia) is a leguminous plant that infests soybean fields in the southeastern United States. Its seeds contain a variety of toxic, highly colored compounds, mainly anthraquinones together with a small amount of fat. These compounds contaminate and lower the quality of soybean oil when inadequately cleaned soybean seed from this area is processed. The sorting of sicklepod seed from a soybean harvest is an additional economic burden on the farmer beyond the cost of proper disposal of the weed seed to avoid worsening field infestation. Fortunately, sicklepod seed also contains substantial amounts of carbohydrates and proteins. These edible components when freed from anthraquinones have a market in pet food as well as potential in human foods because of the high galactomannan ratio of the polysaccharides. Sicklepod seed was dehulled, and the ground endosperm was defatted, followed by sequential solvent extraction of the defatted seed meal to isolate the anthraquinones, carbohydrates, and protein components into their respective classes. Each class of isolate was spectroscopically identified.

The effect of obesity on the contractile performance of isolated mouse soleus, EDL, and diaphragm muscles.

PubMed

Tallis, Jason; Hill, Cameron; James, Rob S; Cox, Val M; Seebacher, Frank

2017-01-01

Obesity affects the major metabolic and cellular processes involved in skeletal muscle contractility. Surprisingly, the effect of obesity on isolated skeletal muscle performance remains unresolved. The present study is the first to examine the muscle-specific changes in contractility following dietary-induced obesity using an isolated muscle work-loop (WL) model that more closely represents in vivo muscle performance. Following 16-wk high-calorific feeding, soleus (SOL), extensor digitorum longus (EDL), and diaphragm (DIA) were isolated from female (CD-1) mice, and contractile performance was compared against a lean control group. Obese SOL produced greater isometric force; however, isometric stress (force per unit muscle area), absolute WL power, and normalized WL power (watts per kilogram muscle mass) were unaffected. Maximal isometric force and absolute WL power of the EDL were similar between groups. For both EDL and DIA, isometric stress and normalized WL power were reduced in the obese groups. Obesity caused a significant reduction in fatigue resistance in all cases. Our findings demonstrate a muscle-specific reduction in contractile performance and muscle quality that is likely related to in vivo mechanical role, fiber type, and metabolic profile, which may in part be related to changes in myosin heavy chain expression and AMP-activated protein kinase activity. These results infer that, beyond the additional requirement of moving a larger body mass, functional performance and quality of life may be further limited by poor muscle function in obese individuals. As such, a reduction in muscle performance may be a substantial contributor to the negative cycle of obesity. The effect of obesity on isolated muscle function is surprisingly underresearched. The present study is the first to examine the effects of obesity on isolated muscle performance using a method that more closely represents real-world muscle function. This work uniquely establishes a muscle-specific profile of mechanical changes in relation to underpinning mechanisms. These findings may be important to understanding the negative cycle of obesity and in designing interventions for improving weight status. Copyright © 2017 the American Physiological Society.

Method for isolating nucleic acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurt, Jr., Richard Ashley; Elias, Dwayne A.

The current disclosure provides methods and kits for isolating nucleic acid from an environmental sample. The current methods and compositions further provide methods for isolating nucleic acids by reducing adsorption of nucleic acids by charged ions and particles within an environmental sample. The methods of the current disclosure provide methods for isolating nucleic acids by releasing adsorbed nucleic acids from charged particles during the nucleic acid isolation process. The current disclosure facilitates the isolation of nucleic acids of sufficient quality and quantity to enable one of ordinary skill in the art to utilize or analyze the isolated nucleic acids formore » a wide variety of applications including, sequencing or species population analysis.« less

Laser capture microdissection of embryonic cells and preparation of RNA for microarray assays.

PubMed

Redmond, Latasha C; Pang, Christopher J; Dumur, Catherine; Haar, Jack L; Lloyd, Joyce A

2014-01-01

In order to compare the global gene expression profiles of different embryonic cell types, it is first necessary to isolate the specific cells of interest. The purpose of this chapter is to provide a step-by-step protocol to perform laser capture microdissection (LCM) on embryo samples and obtain sufficient amounts of high-quality RNA for microarray hybridizations. Using the LCM/microarray strategy on mouse embryo samples has some challenges, because the cells of interest are available in limited quantities. The first step in the protocol is to obtain embryonic tissue, and immediately cryoprotect and freeze it in a cryomold containing Optimal Cutting Temperature freezing media (Sakura Finetek), using a dry ice-isopentane bath. The tissue is then cryosectioned, and the microscope slides are processed to fix, stain, and dehydrate the cells. LCM is employed to isolate specific cell types from the slides, identified under the microscope by virtue of their morphology. Detailed protocols are provided for using the currently available ArcturusXT LCM instrument and CapSure(®) LCM Caps, to which the selected cells adhere upon laser capture. To maintain RNA integrity, upon removing a slide from the final processing step, or attaching the first cells on the LCM cap, LCM is completed within 20 min. The cells are then immediately recovered from the LCM cap using a denaturing solution that stabilizes RNA integrity. RNA is prepared using standard methods, modified for working with small samples. To ensure the validity of the microarray data, the quality of the RNA is assessed using the Agilent bioanalyzer. Only RNA that is of sufficient integrity and quantity is used to perform microarray assays. This chapter provides guidance regarding troubleshooting and optimization to obtain high-quality RNA from cells of limited availability, obtained from embryo samples by LCM.

Laser Capture Microdissection of Embryonic Cells and Preparation of RNA for Microarray Assays

PubMed Central

Redmond, Latasha C.; Pang, Christopher J.; Dumur, Catherine; Haar, Jack L.; Lloyd, Joyce A.

2014-01-01

In order to compare the global gene expression profiles of different embryonic cell types, it is first necessary to isolate the specific cells of interest. The purpose of this chapter is to provide a step-by-step protocol to perform laser capture microdissection (LCM) on embryo samples and obtain sufficient amounts of high-quality RNA for microarray hybridizations. Using the LCM/microarray strategy on mouse embryo samples has some challenges, because the cells of interest are available in limited quantities. The first step in the protocol is to obtain embryonic tissue, and immediately cryoprotect and freeze it in a cryomold containing Optimal Cutting Temperature freezing media (Sakura Finetek), using a dry ice–isopentane bath. The tissue is then cryosectioned, and the microscope slides are processed to fix, stain, and dehydrate the cells. LCM is employed to isolate specific cell types from the slides, identified under the microscope by virtue of their morphology. Detailed protocols are provided for using the currently available ArcturusXT LCM instrument and CapSure® LCM Caps, to which the selected cells adhere upon laser capture. To maintain RNA integrity, upon removing a slide from the final processing step, or attaching the first cells on the LCM cap, LCM is completed within 20 min. The cells are then immediately recovered from the LCM cap using a denaturing solution that stabilizes RNA integrity. RNA is prepared using standard methods, modified for working with small samples. To ensure the validity of the microarray data, the quality of the RNA is assessed using the Agilent bioanalyzer. Only RNA that is of sufficient integrity and quantity is used to perform microarray assays. This chapter provides guidance regarding troubleshooting and optimization to obtain high-quality RNA from cells of limited availability, obtained from embryo samples by LCM. PMID:24318813

The first external quality assessment of isolation and identification of influenza viruses in cell culture in the Asia Pacific region, 2016.

PubMed

Reading, Patrick C; Leung, Vivian K; Buettner, Iwona; Gillespie, Leah; Deng, Yi-Mo; Shaw, Robert; Spirason, Natalie; Todd, Angela; Shah, Aparna Singh; Konings, Frank; Barr, Ian G

2017-12-01

The isolation and propagation of influenza viruses from clinical specimens are essential tools for comprehensive virologic surveillance. Influenza viruses must be amplified in cell culture for detailed antigenic analysis and for phenotypic assays assessing susceptibility to antiviral drugs or for other assays. To conduct an external quality assessment (EQA) of proficiency for isolation and identification of influenza viruses using cell culture techniques among National Influenza Centres (NICs) in the World Health Organisation (WHO) South East Asia and Western Pacific Regions. Twenty-one NICs performed routine influenza virus isolation and identification techniques on a proficiency testing panel comprising 16 samples, containing influenza A or B viruses and negative control samples. One sample was used exclusively to determine their capacity to measure hemagglutination titer and the other 15 samples were used for virus isolation and identification. All NICs performed influenza virus isolation using Madin Darby canine kidney (MDCK) or MDCK-SIAT-1 cells. If virus growth was detected, the type, subtype and/or lineage of virus present in isolates was determined using immunofluorescence, RT-PCR and/or hemagglutination inhibition (HI) assays. Most participating laboratories could detect influenza virus growth and could identify virus amplified from EQA samples. However, some laboratories failed to isolate and identify viruses from EQA samples that contained lower titres of virus, highlighting issues regarding the sensitivity of influenza virus isolation methods between laboratories. This first round of EQA was successfully conducted by NICs in the Asia Pacific Region, revealing good proficiency in influenza virus isolation and identification. Copyright © 2017 Elsevier B.V. All rights reserved.

Report of reprocessing of reflection seismic profile X-5 Waste Isolation Pilot Plant site, Eddy County, New Mexico

USGS Publications Warehouse

Miller, John J.

1983-01-01

Seismic reflection profile X-5 exhibits a 7,700 ft long anomalous zone of poor quality to nonexistent reflections between shotpoints 100 and 170, compared to the high-quality, flat-lying, coherent reflections on either side. Results from drill holes in the area suggest 'layer cake' geology with no detectable abnormalities such as faults present. In an attempt to determine whether the anomalous zone of the seismic profile is an artifact or actually indicates a geologic condition, the data were extensively reprocessed using state-of-the-art processing techniques and the following conclusions were made: 1. The field-recorded data in the anomalous zone are of poor quality due to surface conditions and recording parameters used. 2. Reprocessing shows reflectors throughout the anomalous zone at all levels. However, it cannot prove that the reflectors are continuous throughout the anomalous zone. 3. Significant improvement in data quality may be achieved if the line is reshot using carefully determined recording parameters.

Are commercial providers a viable option for clinical bacterial sequencing?

PubMed

Raven, Kathy; Blane, Beth; Churcher, Carol; Parkhill, Julian; Peacock, Sharon J

2018-04-05

Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.

Morphology, crystallinity, pasting, thermal and quality characteristics of starches from adzuki bean (Vigna angularis L.) and edible kudzu (Pueraria thomsonii Benth).

PubMed

Reddy, Chagam Koteswara; Luan, Fei; Xu, Baojun

2017-12-01

Starches were isolated from adzuki bean (Vigna angularis L.) and edible kudzu (Pueraria thomsonii Benth) and investigated for their physico-chemical, morphological, pasting, crystallinity, thermal and FT-IR spectroscopic characteristics. Statistical analysis of physico-chemical and functional characteristics showed significant (p<0.05) difference between isolated starches from adzuki bean and edible kudzu. The XRD pattern of starches from adzuki bean and edible kudzu showed A-type with reflections (2θ) at 15.0°, 17.03°, 17.89°, 23.18°and 15.12°, 17.03°, 17.77°, 23.3°, respectively. The starch granules from adzuki bean were smooth, round, oval to kidney or irregular while those of edible kudzu starch were spherical, hemispherical and polygonal. Edible kudzu starch exhibited high pasting temperature, gelatinization temperatures, enthalpy and less pasting parameters as compared to starch from adzuki bean. Peaks in FT-IR spectra of both starches shown its carbohydrate nature. Starch from adzuki bean showed high swelling power and solubility as compared to edible kudzu, and enhanced the swelling power and solubility of isolated starches with the temperature raised from 50°C and 90°C. Finally, this work offers data for the application of starches isolated from adzuki bean and edible kudzu that would be applicable for both food and non-food industries. Copyright © 2017 Elsevier B.V. All rights reserved.

An Isolator System for minimally invasive surgery: the new design

PubMed Central

Jansen, Frank-Willem; Dankelman, Jenny

2010-01-01

Background The risk of obtaining a postsurgical infection depends highly on the air quality surrounding the exposed tissue, surgical instruments, and materials. Many isolators for open surgery have been invented to create a contained sterile volume around the exposed tissue. With the use of an isolator, a surgical procedure can be performed outside sterile environments. The goal of this study was to design an Isolator System (IS) for standard laparoscopic instruments while instrument movements are not restricted. Methods The developed IS consists of a sleeve to protect the instrument shaft and tip and a special balloon to protect the incision and trocar tube. A coupling mechanism connected at the sleeve allows instrument changes without contamination of the isolated parts. Smoke tests were performed to show that outside air does not enter the new IS during a simulated laparoscopic procedure. Eight test runs and one baseline run inside a contained volume filled with thick smoke were performed to investigate whether smoke particles entered the Isolator System. Filters were used to identify smoke entering the Isolator System. Results Seven filters showed no trace of smoke particles. In one test run, a part of the IS loosened and a small brown spot was visible. The filter from the baseline run was completely covered with a thick layer of particles, proving the effectiveness of the test. During all test runs, the isolated instrument was successfully locked on and unlocked from the isolated trocar. Instrument movements gave no complications. After removal of the isolated instrument, it took three novices an average of 3.1 (standard deviation (SD), 0.7) seconds to replace it correctly on the isolated trocar. Conclusions The designed IS for laparoscopy can increase sterility in environments where sterility cannot be guaranteed. The current design is developed for laparoscopy, but it can easily be adapted for other fields in minimally invasive surgery. PMID:20108141

Wavelet methodology to improve single unit isolation in primary motor cortex cells.

PubMed

Ortiz-Rosario, Alexis; Adeli, Hojjat; Buford, John A

2015-05-15

The proper isolation of action potentials recorded extracellularly from neural tissue is an active area of research in the fields of neuroscience and biomedical signal processing. This paper presents an isolation methodology for neural recordings using the wavelet transform (WT), a statistical thresholding scheme, and the principal component analysis (PCA) algorithm. The effectiveness of five different mother wavelets was investigated: biorthogonal, Daubachies, discrete Meyer, symmetric, and Coifman; along with three different wavelet coefficient thresholding schemes: fixed form threshold, Stein's unbiased estimate of risk, and minimax; and two different thresholding rules: soft and hard thresholding. The signal quality was evaluated using three different statistical measures: mean-squared error, root-mean squared, and signal to noise ratio. The clustering quality was evaluated using two different statistical measures: isolation distance, and L-ratio. This research shows that the selection of the mother wavelet has a strong influence on the clustering and isolation of single unit neural activity, with the Daubachies 4 wavelet and minimax thresholding scheme performing the best. Copyright © 2015. Published by Elsevier B.V.

Comparison of isolate dadih with yeast dadih in improving nutrition quality of Cassava Waste (CW)

NASA Astrophysics Data System (ADS)

Ginting, N.

2018-03-01

The cassava industry in North Sumatra Province was one of the most significant agricultural industries. Waste from the cassava industry which was called cassava waste/CW/Onggok was used as feed for ruminants such as cattle, sheep and monogastric such as pigs. The low nutrients in CW caused the need to find a way for improving the nutrients quality. This research was conducted with the aim to help livestockers to ferment their livestock feed. This study compared the ability of fermentation between dadih isolate with dadih yeast. Dadih is traditional food in Indonesia where milk is fermented in bamboo tube. Dadih yeast was made by mixing dadih and whey with flour, made in around shape and sun dried. The results showed that pH of CW by dadih isolate was the lowest while crude protein, crude fiber and fat in CW treated with dadih isolate were improved significantly compared either to control or to dadih starter while fermented CW was better than non-fermented CW. It was recommended livestockers to ferment CW by using either by dadih isolate or dadih starter.

3D/2D image registration method for joint motion analysis using low-quality images from mini C-arm machines

NASA Astrophysics Data System (ADS)

Ghafurian, Soheil; Hacihaliloglu, Ilker; Metaxas, Dimitris N.; Tan, Virak; Li, Kang

2017-03-01

A 3D kinematic measurement of joint movement is crucial for orthopedic surgery assessment and diagnosis. This is usually obtained through a frame-by-frame registration of the 3D bone volume to a fluoroscopy video of the joint movement. The high cost of a high-quality fluoroscopy imaging system has hindered the access of many labs to this application. This is while the more affordable and low-dosage version, the mini C-arm, is not commonly used for this application due to low image quality. In this paper, we introduce a novel method for kinematic analysis of joint movement using the mini C-arm. In this method the bone of interest is recovered and isolated from the rest of the image using a non-rigid registration of an atlas to each frame. The 3D/2D registration is then performed using the weighted histogram of image gradients as an image feature. In our experiments, the registration error was 0.89 mm and 2.36° for human C2 vertebra. While the precision is still lacking behind a high quality fluoroscopy machine, it is a good starting point facilitating the use of mini C-arms for motion analysis making this application available to lower-budget environments. Moreover, the registration was highly resistant to the initial distance from the true registration, converging to the answer from anywhere within +/-90° of it.

A New Approach to Look at the Electrical Conductivity of Streamflow: Decomposing a Bulk Signal to Recover Individual Solute Concentrations at High-Frequency

NASA Astrophysics Data System (ADS)

Benettin, P.; Van Breukelen, B. M.

2017-12-01

The ability to evaluate stream hydrochemistry is often constrained by the capacity to sample streamwater at an adequate frequency. While technology is no longer a limiting factor, economic and management efforts can still be a barrier to high-resolution water quality instrumentation. We propose a new framework to investigate the electrical conductivity (EC) of streamwater, which can be measured continuously through inexpensive sensors. We show that EC embeds information on ion content which can be isolated to retrieve solute concentrations at high resolution. The approach can already be applied to a number of datasets worldwide where water quality campaigns are conducted, provided continuous EC measurements can be collected. The essence of the approach is the decomposition of the EC signal into its "harmonics", i.e. the specific contributions of the major ions which conduct current in water. The ion contribution is used to explore water quality patterns and to develop algorithms that reconstruct solute concentrations during periods where solute measurements are not available. The approach is validated on a hydrochemical dataset from Plynlimon, Wales. Results show that the decomposition of EC is feasible and for at least two major elements the methodology provided improved estimates of high-frequency solute dynamics. Our results support the installation of EC probes to complement water quality campaigns and suggest that the potential of EC measurements in rivers is currently far from being fully exploited.

Patient experience of source isolation: lessons for clinical practice.

PubMed

Barratt, Ruth Linda; Shaban, Ramon; Moyle, Wendy

2011-10-01

Methicillin-resistant Staphylococcus aureus (MRSA) is now the leading antimicrobial-resistant organism of concern to clinicians worldwide. Preventing and controlling the increase and spread of MRSA within the health-care environment is therefore an important function of the infection control team. The prevention and control of MRSA requires strict use of both Standard and Additional Precautions, which include good hand hygiene practices, judicious antimicrobial prescribing, and source isolation. While few would dispute the need for these precautions for preventing the spread of MRSA and other infections, their use may result in adverse physical and psychological effects for the patient. In an age of quality and safety of health care, ensuring infection control practice such as source isolation and contact precautions adhere to fundamental human rights is paramount. This paper presents a review of the literature on the patient experience of source isolation for MRSA or other infectious diseases. The review yielded five major interconnected themes: (1) psychological effects of isolation; (2) coping with isolation; (3) social isolation; (4) communication and information provision; and (5) physical environment and quality of care. It found that the experience of isolation by patients has both negative and positive elements. Isolation may result in detrimental psychological effects including anxiety, stress and depression, but may also result in the patient receiving less or substandard care. However, patients may also benefit from the quietness and privacy of single rooms. Nurses and other healthcare workers must look for ways to improve the experience of isolation and contact precautions of patients in source isolation. Opportunities exist in particular in improving the environment and the patient's self-control of the situation and in providing adequate information.

DEVELOPING A REGULATORY PROGRAM FOR ISOLATED WETLANDS IN WASHINGTON

EPA Science Inventory

The Supreme Court's recent decision on isolated wetlands leaves many wetlands in Washington unprotected. Previously these wetlands were regulated through use of state-issued CWA ?401 water quality certifications, during the Corps of Engineers ?404 permitting process. But since ...

Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice.

PubMed

Suh, Jung-Pil; Jeung, Ji-Ung; Noh, Tae-Hwan; Cho, Young-Chan; Park, So-Hyun; Park, Hyun-Su; Shin, Mun-Sik; Kim, Chung-Kon; Jena, Kshirod K

2013-02-08

The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will have a high impact on the yield stability and sustainability of rice productivity.

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents.

PubMed

Benson, Courtney A; Bizzoco, Richard W; Lipson, David A; Kelley, Scott T

2011-04-01

Fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. Recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to DNA isolation. In this study, we report the development of novel DNA isolation approaches for fumarole deposit microbial community analysis. Deposit samples were collected from steam vents and caves in Hawaii Volcanoes National Park, Yellowstone National Park and Lassen Volcanic National Park. Samples were analyzed by X-ray microanalysis and classified as nonsulfur, sulfur or iron-dominated steam deposits. We experienced considerable difficulty in obtaining high-yield, high-quality DNA for cloning: only half of all the samples ultimately yielded sequences. Analysis of archaeal 16S rRNA gene sequences showed that sulfur steam deposits were dominated by Sulfolobus and Acidianus, while nonsulfur deposits contained mainly unknown Crenarchaeota. Several of these novel Crenarchaeota lineages were related to chemoautotrophic ammonia oxidizers, indicating that fumaroles represent a putative habitat for ammonia-oxidizing Archaea. We also generated archaeal and bacterial enrichment cultures from the majority of the deposits and isolated members of the Sulfolobales. Our results provide the first evidence of Archaea in geothermal steam deposits and show that fumaroles harbor diverse and novel microbial lineages. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Chronic Social Isolation Enhances Reproduction in the Monogamous Prairie Vole (Microtus ochrogaster)

PubMed Central

Perry, Adam N.; Carter, C. Sue; Cushing, Bruce S.

2016-01-01

Chronic stressors are generally considered to disrupt reproduction and inhibit mating. Here we test the hypothesis that a chronic stressor, specifically social isolation, can facilitate adaptive changes that enhance/accelerate reproductive effort. In general, monogamous species display high levels of prosociality, delayed sexual maturation, and greater parental investment in fewer, higher quality offspring compared with closely related polygynous species. We predicted that chronic social isolation would promote behavioral and neurochemical patterns in prairie voles associated with polygyny. Male and female prairie voles were isolated for four weeks and changes in mating behavior, alloparental care, estrogen receptor (ER) α expression and tyrosine hydroxylase (TH) expression in brain regions regulating sociosexual behavior were examined. In males, isolation accelerated copulation, increased ERα in the medial amygdala (MEApd) and bed nucleus of the stria terminalis (BSTpm), and reduced TH expression in the MEApd and BSTpm, but had no effect on alloparental behavior. In females, isolation resulted in more rapid estrus induction and reduced TH expression in the MEApd and BSTpm, but had no effect on estradiol sensitivity or ERα expression. The results support the hypothesis that ERα expression in the MEApd and BSTpm is a critical determinant of male copulatory behavior and/or mating system. The lack of change in alloparental behavior suggests that changes in prosocial behavior are selective and regulated by different mechanisms. The results also suggest that TH in the MEApd and BSTpm may play a critical role in determining mating behavior in both sexes. PMID:26939085

Biopotentiality of High Efficient Aerobic Denitrifier Bacillus megaterium S379 for Intensive Aquaculture Water Quality Management.

PubMed

Gao, Junqian; Gao, Dan; Liu, Hao; Cai, Jiajai; Zhang, Junqi; Qi, Zhengliang

2018-05-24

Excessive nitrite accumulation is a very tough issue for intensive aquaculture. A high efficient aerobic denitrifier Bacillus megaterium S379 with 91.71±0.17% of NO 2 - -N (65 mg L -1 ) removal was successfully isolated for solving the problem. Denitrification of S379 showed excellent environment adaptation that it kept high nitrite removal ratio (more than 85%) when temperature ranged from 25°C to 40°C and pH varied between 7.0 and 9.0, and could endure as high as 560 mg L -1 of NO 2 - -N. Immobilization of S379 could enhance denitrification even when NO 2 - -N adding amount got to 340 mg L -1 . Immobilized cells also showed well pollutants removal performance in aquaculture wastewater treatment. Moreover, S379 possessed positive hydrolase activities for starch, casein, cellulose and fat and bore more than 60 ppt of salinity. Totally, all the results revealed significant potentiality of immobilized S379 applied in aquaculture water quality management. Copyright © 2018 Elsevier Ltd. All rights reserved.

Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

PubMed Central

Beaton, Ainsley; Lood, Cédric; Cunningham-Oakes, Edward; MacFadyen, Alison; Mullins, Alex J; Bestawy, Walid El; Botelho, João; Chevalier, Sylvie; Dalzell, Chloe; Dolan, Stephen K; Faccenda, Alberto; Ghequire, Maarten G K; Higgins, Steven; Kutschera, Alexander; Murray, Jordan; Redway, Martha; Salih, Talal; Smith, Brian A; Smits, Nathan; Thomson, Ryan; Woodcock, Stuart; Cornelis, Pierre; Lavigne, Rob; van Noort, Vera

2018-01-01

Abstract Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline. PMID:29579234

Increased sensitivity of RT-PCR for Potato virus Y detection using RNA isolated by a procedure with differential centrifugation.

PubMed

Zhang, Jianhua; Nie, Xianzhou; Boquel, Sébastien; Al-Daoud, Fadi; Pelletier, Yvan

2015-12-01

The sensitivity of reverse transcription-polymerase chain reaction (RT-PCR) for virus detection is influenced by many factors such as specificity of primers and quality of templates. These factors become extremely important for successful detection when virus concentration is low. Total RNA isolated from Potato virus Y (PVY)-infected potato plants using the sodium sulfite RNA isolation method or RNeasy plant mini kit contains a high proportion of host RNA and may also contain trace amount of phenolic and polysaccharide residues, which may inhibit RT-PCR. The goal of this study was to enhance the sensitivity of PVY detection by reducing host RNA in the extract by differential centrifugation followed by extraction using an RNeasy mini kit (DCR method). One-step RT-PCR had relatively low amplification efficiency for PVY RNA when a high proportion of plant RNA was present. SYBR Green-based real time RT-PCR showed that the RNA isolated by the DCR method had a higher cycle threshold value (Ct) for the elongation factor 1-α mRNA (Ef1α) of potato than the Ct value of the RNA extracted using the RNeasy plant mini kit, indicating that the DCR method significantly reduced the proportion of potato RNA in the extract. The detectable amount of RNA extracted using the DCR method was <0.001ng when plant sap from 10 PVY-infected and PVY-free potato leaflets in a 1.5:100 fresh weight ratio was extracted, compared with 0.01 and 0.02ng of RNA using the RNeasy plant mini kit and sodium sulfite RNA isolation methods, respectively. Copyright © 2015. Published by Elsevier B.V.

Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains.

PubMed Central

Toledo, G; Palenik, B

1997-01-01

Because they are ubiquitous in a range of aquatic environments and culture methods are relatively advanced, cyanobacteria may be useful models for understanding the extent of evolutionary adaptation of prokaryotes in general to environmental gradients. The roles of environmental variables such as light and nutrients in influencing cyanobacterial genetic diversity are still poorly characterized, however. In this study, a total of 15 Synechococcus strains were isolated from the oligotrophic edge of the California Current from two depths (5 and 95 m) with large differences in light intensity, light quality, and nutrient concentrations. RNA polymerase gene (rpoC1) fragment sequences of the strains revealed two major genetic lineages, distinct from other marine or freshwater cyanobacterial isolates or groups seen in shotgun-cloned sequences from the oligotrophic Atlantic Ocean. The California Current low-phycourobilin (CCLPUB) group represented by six isolates in a single lineage was less diverse than the California Current high-phycourobilin (CCHPUB) group with nine isolates in three relatively divergent lineages. The former was found to be the closest known genetic group to Prochlorococcus spp., a chlorophyll b-containing cyanobacterial group. Having an isolate from this group will be valuable for looking at the molecular changes necessary for the transition from the use of phycobiliproteins to chlorophyll b as light-harvesting pigments. Both of the CCHPUB and CCLPUB groups included strains obtained from surface (5 m) and deep (95 m) samples. Thus, contrary to expectations, there was no clear correlation between sampling depth and isolation of genetic groups, despite the large environmental gradients present. To our knowledge, this is the first demonstration with isolates that genetically divergent Synechococcus groups coexist in the same seawater sample. PMID:9361417

Polymyxin B Etest® compared with gold-standard broth microdilution in carbapenem-resistant Enterobacteriaceae exhibiting a wide range of polymyxin B MICs.

PubMed

Kulengowski, B; Ribes, J A; Burgess, D S

2018-04-16

Polymyxins have been revitalized to combat carbapenem-resistant Enterobacteriaceae (CRE). However, evaluating the activity of these agents by traditional broth dilution methods is not practical for busy clinical laboratories. We compared polymyxin B activity using two quantitative susceptibility testing methods, Etest ® and broth microdilution (BMD), against CRE isolates from patients at an academic medical centre. Polymyxin B activity against 70 CRE clinical isolates was determined by Etest ® according to the manufacturer and by BMD according to CLSI guidelines. Pseudomonas aeruginosa ATCC ® 27853 and Escherichia coli NCTC 13846 served as quality control strains. The EUCAST colistin susceptibility breakpoint of Enterobacteriaceae (≤2 mg/L) was used. Essential agreement was isolates with an MIC within 1 log 2 dilution over total isolates. Categorical agreement was number of isolates in the same susceptibility category (susceptible or resistant) over total isolates. Major and very major error rates were calculated using number of susceptible and number of resistant isolates, respectively, as the denominator. McNemar's test was used for determining a difference in susceptibility between methods. The CRE isolates were primarily Klebsiella spp. (49%) and Enterobacter spp. (36%). Polymyxin B susceptibility was significantly higher by Etest ® compared with BMD (97% versus 77%; p 0.0001). Categorical agreement was 80%, but essential agreement was low (10%). False non-susceptibility was never observed by Etest ® (BMD reference), but the very major errors were high (88%). Etest ® reporting of false susceptibility may result in inappropriate antibiotic use and treatment failure clinically. We do not recommend using Etest ® for polymyxin B susceptibility testing for routine patient care. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Seasonal stability of Cladophora-associated Salmonella in Lake Michigan watersheds.

PubMed

Byappanahalli, Muruleedhara N; Sawdey, Richard; Ishii, Satoshi; Shively, Dawn A; Ferguson, John A; Whitman, Richard L; Sadowsky, Michael J

2009-02-01

The bacterial pathogens Shigella, Salmonella, Campylobacter, and shiga toxin-producing E. coli (STEC) were recently found to be associated with Cladophora growing in southern Lake Michigan. Preliminary results indicated that the Salmonella strains associated with Cladophora were genetically identical to each other. However, because of the small sample size (n=37 isolates) and a lack of information on spatial-temporal relationships, the nature of the association between Cladophora and Salmonella remained speculative. In this study, we investigated the population structure and genetic relatedness of a large number of Cladophora-borne Salmonella isolates from Lake Michigan (n=133), as well as those isolated from stream and lake water (n=31), aquatic plants (n=8), and beach sands and sediments (n=8) from adjacent watersheds. Salmonella isolates were collected during 2005-2007 between May and August from Lake Michigan beachsheds in Wisconsin, Illinois, and Indiana. The genetic relatedness of Salmonella isolates was examined by using the horizontal, fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. While the Salmonella isolates associated with Cladophora exhibited a high degree of genetic relatedness (>or=92% similarity), the isolates were not all genetically identical. Spatial and temporal relationships were evident in the populations examined, with tight clustering of the isolates both by year and location. These findings suggest that the relationship between Salmonella and Cladophora is likely casual and is related to input sources (e.g. wastewater, runoff, birds) and the predominant Salmonella genotype surviving in the environment during a given season. Our studies indicate that Cladophora is likely an important reservoir for Salmonella and other enteric bacterial pathogens in Lake Michigan beachsheds, which in turn may influence nearshore water quality.

Seasonal stability of Cladophora-associated Salmonella in Lake Michigan watersheds

USGS Publications Warehouse

Byappanahalli, M.N.; Sawdey, R.; Ishii, S.; Shively, D.A.; Ferguson, J.A.; Whitman, R.L.; Sadowsky, M.J.

2009-01-01

The bacterial pathogens Shigella, Salmonella, Campylobacter, and shiga toxin-producing E. coli (STEC) were recently found to be associated with Cladophora growing in southern Lake Michigan. Preliminary results indicated that the Salmonella strains associated with Cladophora were genetically identical to each other. However, because of the small sample size (n = 37 isolates) and a lack of information on spatial-temporal relationships, the nature of the association between Cladophora and Salmonella remained speculative. In this study, we investigated the population structure and genetic relatedness of a large number of Cladophora-borne Salmonella isolates from Lake Michigan (n = 133), as well as those isolated from stream and lake water (n = 31), aquatic plants (n = 8), and beach sands and sediments (n = 8) from adjacent watersheds. Salmonella isolates were collected during 2005-2007 between May and August from Lake Michigan beachsheds in Wisconsin, Illinois, and Indiana. The genetic relatedness of Salmonella isolates was examined by using the horizontal, fluorophore-enhanced rep-PCR (HFERP) DNA fingerprinting technique. While the Salmonella isolates associated with Cladophora exhibited a high degree of genetic relatedness (???92% similarity), the isolates were not all genetically identical. Spatial and temporal relationships were evident in the populations examined, with tight clustering of the isolates both by year and location. These findings suggest that the relationship between Salmonella and Cladophora is likely casual and is related to input sources (e.g. wastewater, runoff, birds) and the predominant Salmonella genotype surviving in the environment during a given season. Our studies indicate that Cladophora is likely an important reservoir for Salmonella and other enteric bacterial pathogens in Lake Michigan beachsheds, which in turn may influence nearshore water quality. ?? 2008 Elsevier Ltd.

Abundance and characteristics of the recreational water quality indicator bacteria Escherichia coli and enterococci in gull faeces

USGS Publications Warehouse

Fogarty, L.R.; Haack, S.K.; Wolcott, M.J.; Whitman, R.L.

2003-01-01

Aims: To evaluate the numbers and selected phenotypic and genotypic characteristics of the faecal indicator bacteria Escherichia coli and enterococci in gull faeces at representative Great Lakes swimming beaches in the United States. Methods and Results: E. coli and enterococci were enumerated in gull faeces by membrane filtration. E. coli genotypes (rep-PCR genomic profiles) and E. coli (Vitek?? GNI+) and enterococci (API?? rapid ID 32 Strep and resistance to streptomycin, gentamicin, vancomycin, tetracycline and ampicillin) phenotypes were determined for isolates obtained from gull faeces both early and late in the swimming season. Identical E. coli genotypes were obtained only from single gull faecal samples but most faecal samples yielded more than one genotype (median of eight genotypes for samples with 10 isolates). E. coli isolates from the same site that clustered at ???85% similarity were from the same sampling date and shared phenotypic characteristics, and at this similarity level there was population overlap between the two geographically isolated beach sites. Enterococcus API?? profiles varied with sampling date. Gull enterococci displayed wide variation in antibiotic resistance patterns, and high-level resistance to some antibiotics. Conclusions: Gull faeces could be a major contributor of E. coli (105-109 CFU g-1) and enterococci (104-108 CFU g-1) to Great Lakes recreational waters. E. coli and enterococci in gull faeces are highly variable with respect to their genotypic and phenotypic characteristics and may exhibit temporal or geographic trends in these features. Significance and Impact of the Study: The high degree of variation in genotypic or phenotypic characteristics of E. coli or enterococci populations within gull hosts will require extensive sampling for adequate characterization, and will influence methods that use these characteristics to determine faecal contamination sources for recreational waters.

Comparative genomic analysis of two isolates of Vibrio cholerae O1 Ogawa El Tor isolated during outbreak in Mariupol in 2011.

PubMed

Kuleshov, Konstantin V; Kostikova, Anna; Pisarenko, Sergey V; Kovalev, Dmitry A; Tikhonov, Sergey N; Savelievа, Irina V; Saveliev, Vilory N; Vasilieva, Oksana V; Zinich, Liliia S; Pidchenko, Nadiia N; Kulichenko, Alexander N; Shipulin, German A

2016-10-01

Cholera is a water-borne, severe enteric infection essentially caused by toxigenic strains of Vibrio cholera O1 and O139 serogroups. An outbreak of cholera was registered during May-July 2011 in Mariupol, Ukraine, with 33 cholera cases and 25 carriers of cholera. Following this outbreak, the toxigenic strain of V. cholerae 2011EL-301 was isolated from seawater in the recreation area of Taganrog city on the territory of Russia. The aim of our study was to understand genomic features of Mariupol isolates as well as to evaluate hypothesis about possible interconnection between the outbreak of cholera in Mariupol and the single case of isolation of V. cholerae from the Sea of Azov in Russia. Mariupol isolates were phenotypically characterized and subsequently subjected to whole genome sequencing procedure. Phylogenetic analysis based on high-quality SNPs of V. cholera O1 El Tor isolates of the 7th pandemic clade from different regions showed that clinical and environmental isolates from Mariupol outbreak were attributable to a unique phylogenetic clade within wave 3 of V. cholera O1 El Tor isolates and characterized by six clade-specific SNPs. Whereas Taganrog isolate belonged to distantly related clade which allows us to reject the hypothesis of transmission the outbreak strain of V. cholerae O1 from Ukraine to Russia in 2011. Mariupol isolates shared a common ancestor with Haiti\\Nepal-4\\India clade indicating that outbreak progenitor strain most likely originated in the South Asia region and later was introduced to Ukraine. Moreover, genomic data both based on hqSNPs and similarity of virulence-associated mobile genomic elements of Mariupol isolates suggests that environmental and clinical isolates are a part of joint outbreak which confirms the role of contaminated domestic sewage, as an element of the complex chain of infection spread during cholera outbreak. In general, the genome-wide comparative analysis of both genes and genomic regions of epidemiological importance indicates accessory of this isolates to 'new' clone of toxigenic multiple drug resistance atypical variant of V. cholerae O1 El Tor. Copyright © 2016 Elsevier B.V. All rights reserved.

Draft genome sequence of the marine bacterium Streptomyces griseoaurantiacus M045, which produces novel manumycin-type antibiotics with a pABA core component.

PubMed

Li, Fuchao; Jiang, Peng; Zheng, Huajun; Wang, Shengyue; Zhao, Guoping; Qin, Song; Liu, Zhaopu

2011-07-01

Streptomyces griseoaurantiacus M045, isolated from marine sediment, produces manumycin and chinikomycin antibiotics. Here we present a high-quality draft genome sequence of S. griseoaurantiacus M045, the first marine Streptomyces species to be sequenced and annotated. The genome encodes several gene clusters for biosynthesis of secondary metabolites and has provided insight into genomic islands linking secondary metabolism to functional adaptation in marine S. griseoaurantiacus M045.

Specificity of Good Manufacturing Practice (GMP) for Biomedical Cell Products.

PubMed

Tulina, M A; Pyatigorskaya, N V

2018-03-01

The article describes special aspects of Good Manufacturing Practice (GMP) for biomedical cell products (BMCP) that imply high standards of aseptics throughout the entire productio process, strict requirements to donors and to the procedure of biomaterial isolation, guaranty of tracing BMCP products, defining processing procedures which allow to identify BMCP as minimally manipulated; continuous quality control and automation of the control process at all stages of manufacturing, which will ensure product release simultaneously with completion of technological operations.

A decade of aeroacoustic research at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Schmitz, Frederic H.; Mosher, M.; Kitaplioglu, Cahit; Cross, J.; Chang, I.

1988-01-01

The rotorcraft aeroacoustic research accomplishments of the past decade at Ames Research Center are reviewed. These include an extensive sequence of flight, ground, and wind tunnel tests that have utilized the facilities to guide and pioneer theoretical research. Many of these experiments were of benchmark quality. The experiments were used to isolate the inadequacies of linear theory in high-speed impulsive noise research, have led to the development of theoretical approaches, and have guided the emerging discipline of computational fluid dynamics to rotorcraft aeroacoustic problems.

Symptoms, quality of life and level of functioning of traumatized refugees at psychiatric trauma clinic in Copenhagen.

PubMed

Buhman, Cæcilie; Mortensen, Erik Lykke; Lundstrøm, Stine; Ryberg, Jasmina; Nordentoft, Merete; Ekstrøm, Morten

2014-01-01

To characterize physical and mental health in trauma exposed refugees by describing a population of patients with regard to background, mental health history and current health problems; and to identify pre- and post-migratory predictors of mental health. All patients receiving treatment at the Psychiatric Trauma Clinic for Refugees in Copenhagen from April 2008 to February 2010 completed self-rating inventories on symptoms of PTSD, depression and anxiety as well as level of functioning and quality of life before treatment. Then, associations of pre and post migratory factors with mental health were explored using linear and logistic regression and Pearson's correlation coefficients. Among the patients, the prevalence of depression, somatic disease, pain, psychotic symptoms co-existing with PTSD and very low level of functioning was high. Persecution, being an ex-combatant and living currently in social isolation were significantly associated with PTSD arousal symptoms and self-reported pain. New treatment modalities should seek to address all of the symptoms and challenges of the patients including psychotic and somatic symptoms and social isolation, and studies of treatment effect should clarify all co-morbidities so that comparable populations can be included in treatment evaluation studies.

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

PubMed

Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

2015-01-01

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Fish assemblages, connectivity, and habitat rehabilitation in a diked Great Lakes coastal wetland complex

USGS Publications Warehouse

Kowalski, Kurt P.; Wiley, Michael J.; Wilcox, Douglas A.

2014-01-01

Fish and plant assemblages in the highly modified Crane Creek coastal wetland complex of Lake Erie were sampled to characterize their spatial and seasonal patterns and to examine the implications of the hydrologic connection of diked wetland units to Lake Erie. Fyke netting captured 52 species and an abundance of fish in the Lake Erie–connected wetlands, but fewer than half of those species and much lower numbers and total masses of fish were captured in diked wetland units. Although all wetland units were immediately adjacent to Lake Erie, there were also pronounced differences in water quality and wetland vegetation between the hydrologically isolated and lake-connected wetlands. Large seasonal variations in fish assemblage composition and biomass were observed in connected wetland units but not in disconnected units. Reestablishment of hydrologic connectivity in diked wetland units would allow coastal Lake Erie fish to use these vegetated habitats seasonally, although connectivity does appear to pose some risks, such as the expansion of invasive plants and localized reductions in water quality. Periodic isolation and drawdown of the diked units could still be used to mimic intermediate levels of disturbance and manage invasive wetland vegetation.

Microencapsulation of Garcinia fruit extract by spray drying and its effect on bread quality.

PubMed

Ezhilarasi, Perumal Natarajan; Indrani, Dasappa; Jena, Bhabani Sankar; Anandharamakrishnan, Chinnaswamy

2014-04-01

(-)-Hydroxycitric acid (HCA) is the major acid present in the fruit rinds of certain species of Garcinia. HCA has been reported to have several health benefits. As HCA is highly hygroscopic in nature and thermally sensitive, it is difficult to incorporate in foodstuffs. Hence, Garcinia cowa fruit extract was microencapsulated using three different wall materials such as whey protein isolate (WPI), maltodextrin (MD) and a combination of whey protein isolate and maltodextrin (WPI + MD) by spray drying. Further, these microencapsulated powders were evaluated for their impact on bread quality and HCA retention. Maltodextrin (MD) encapsulates had higher free (86%) and net HCA (90%) recovery. Microencapsulates incorporated breads had enhanced qualitative characteristics and higher HCA content than water extract incorporated bread due to efficient encapsulation during bread baking. Comparatively, bread with MD encapsulates showed softer crumb texture, desirable sensory attributes with considerable volume and higher HCA content. The higher HCA contents of encapsulate incorporated breads were sufficient to claim for functionality of HCA in bread. Comparatively, MD had efficiently encapsulated Garcinia fruit extract during spray drying and bread baking. Spray drying proved to be an excellent encapsulation technique for incorporation into the food system. © 2013 Society of Chemical Industry.

Global Measurement of the Quality of Education: A Help to Developing Countries?

ERIC Educational Resources Information Center

Vedder, Paul

1994-01-01

Addresses the involvement of international interest groups in defining and determining educational quality in developing countries, suggesting that global measures of quality damage the educational systems of developing countries by creating feelings of isolation and inferiority. Suggests alternative measures which meet global standards and may be…

Accounting for Unobserved Time-Varying Quality in Recreation Demand: An Application to a Sonoran Desert Wilderness

EPA Science Inventory

Environmental variables can be important factors in recreation demand. Analysts wishing to quantify environmental quality impacts face the difficult issue of isolating them from unobserved variables. Quality changes may occur in space, varying between sites, or in time, varying b...

Partners | Integrated Energy Solutions | NREL

Science.gov Websites

Develops Off-Grid Energy Access through Quality Assurance Framework for Mini-Grids NREL has teamed with the Africa to develop a Quality Assurance Framework for isolated mini-grids. NREL Enhances Energy Resiliency Partnership Develops Off-Grid Energy Access through Quality Assurance Framework for Mini-Grids NREL has teamed

Isolation of anacardic acid from natural cashew nut shell liquid (CNSL) using supercritical carbon dioxide.

PubMed

Philip, Joseph Y N; Da Cruz Francisco, José; Dey, Estera S; Buchweishaija, Joseph; Mkayula, Lupituko L; Ye, Lei

2008-10-22

Solvent extracted cashew nut shell liquid (CNSL), conventionally known as natural CNSL, is a mixture of several alkenyl phenols. One of these alkenyl phenols is anacardic acid, which is present at the highest concentration. In view of anticipated industrial applications of anacardic acid, the objective of this work was to isolate anacardic acid from natural CNSL by supercritical carbon dioxide (scCO 2). In this study, the solubility data for natural CNSL in scCO 2 under a range of operating conditions of pressure (100, 200, and 300 bar), temperature (40 and 50 degrees C), and CO 2 flow rate (5, 10, and 15 g min (-1)) were established. The best scCO 2 working conditions were found to be 50 degrees C and 300 bar at a flow rate of 5 g min (-1) CO 2. Using 3 g of sample (CNSL/solid adsorbent = 1/2) under these scCO 2 conditions, it was possible to quantitatively isolate high purity anacardic acid from crude natural CNSL (82% of total anacardic acid) within 150 min. The anacardic acid isolated by scCO 2 was analyzed by different spectroscopic techniques (UV-vis, FT-IR, and (1)H NMR) and HPLC analysis, indicating that the anacardic acid isolated by scCO 2 has better quality than that obtained through a conventional method involving several chemical conversion steps.

Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce.

PubMed

Cook, Kimberly L; Givan, Ethan C; Mayton, Holly M; Parekh, Rohan R; Taylor, Ritchie; Walker, Sharon L

2017-12-04

Despite continuing efforts to reduce foodborne pathogen contamination of fresh produce, significant outbreaks continue to occur. Identification of appropriate surrogates for foodborne pathogens facilitates relevant research to identify reservoirs and amplifiers of these contaminants in production and processing environments. Therefore, the objective of this study was to identify environmental Escherichia coli isolates from manures (poultry, swine and dairy) and surface water sources with properties similar to those of the produce associated foodborne pathogens E. coli O157:H7 and Salmonella enterica serotype Typhimurium. The most similar environmental E. coli isolates were from poultry (n=3) and surface water (n=1) sources. The best environmental E. coli surrogates had cell surface characteristics (zeta potential, hydrophobicity and exopolysaccharide composition) that were similar (i.e., within 15%) to those of S. Typhimurium and/or formed biofilms more often when grown in low nutrient media prepared from lettuce lysates (24%) than when grown on high nutrient broth (7%). The rate of attachment of environmental isolates to lettuce leaves was also similar to that of S. Typhimurium. In contrast, E. coli O157:H7, a commonly used E. coli quality control strain and swine isolates behaved similarly; all were in the lowest 10% of isolates for biofilm formation and leaf attachment. These data suggest that the environment may provide a valuable resource for selection of surrogates for foodborne pathogens. Published by Elsevier B.V.

The effect of anaerobic fungal inoculation on the fermentation characteristics of rice straw silages.

PubMed

Lee, S M; Guan, L L; Eun, J-S; Kim, C-H; Lee, S J; Kim, E T; Lee, S S

2015-03-01

To identify whether the supplement of anaerobic fungi isolates with cellulolytic activities accelerates the silage fermentation. Three fungal isolates with the highest cellulolytic activities among 45 strains of anaerobic fungal stock in our laboratory were selected and used as silage inoculants. The rice straw (RS) was ensiled for 10, 30, 60, 90 and 120 days with four treatments of anaerobic fungi derived from the control (no fungus), Piromyces M014 (isolated from the rumen of the Korean native goat), Orpinomyces R001 (isolated from the duodenum of Korean native cattle) and Neocallimastix M010 (isolated from the guts of termites), respectively. The silages inoculated with pure strains of fungi showed a higher fungal population (P < 0.05) when compared to the control silage. In situ ruminal DM disappearance of RS silage (RSS) was improved with fungal treatment. SEM observation showed live fungal cells inoculated in RS could survive during the ensiling process. Overall, this study indicated that the inoculation of anaerobic fungi decreased the cell wall content of the RSS and increased in situ dry matter disappearance. The supplementation of anaerobic fungi isolates to RSS as a silage inoculant improves the RSS quality. This is the first study showing the potential application of supplement of anaerobic fungi isolated from the guts may be applied industrially as an alternate feed additive that improves the silage quality. © 2014 The Society for Applied Microbiology.

Interventions to reduce social isolation and loneliness among older people: an integrative review.

PubMed

Gardiner, Clare; Geldenhuys, Gideon; Gott, Merryn

2018-03-01

Loneliness and social isolation are major problems for older adults. Interventions and activities aimed at reducing social isolation and loneliness are widely advocated as a solution to this growing problem. The aim of this study was to conduct an integrative review to identify the range and scope of interventions that target social isolation and loneliness among older people, to gain insight into why interventions are successful and to determine the effectiveness of those interventions. Six electronic databases were searched from 2003 until January 2016 for literature relating to interventions with a primary or secondary outcome of reducing or preventing social isolation and/or loneliness among older people. Data evaluation followed Evidence for Policy and Practice Information and Co-ordinating Centre guidelines and data analysis was conducted using a descriptive thematic method for synthesising data. The review identified 38 studies. A range of interventions were described which relied on differing mechanisms for reducing social isolation and loneliness. The majority of interventions reported some success in reducing social isolation and loneliness, but the quality of evidence was generally weak. Factors which were associated with the most effective interventions included adaptability, a community development approach, and productive engagement. A wide range of interventions have been developed to tackle social isolation and loneliness among older people. However, the quality of the evidence base is weak and further research is required to provide more robust data on the effectiveness of interventions. Furthermore, there is an urgent need to further develop theoretical understandings of how successful interventions mediate social isolation and loneliness. © 2016 John Wiley & Sons Ltd.

Treatable Bacterial Infections Are Underrecognized Causes of Fever in Ethiopian Children

PubMed Central

Aarsland, Sara J.; Castellanos-Gonzalez, Alejandro; Lockamy, Kameron P.; Mulu-Droppers, Ruth; Mulu, Moges; White, A. Clinton; Cabada, Miguel M.

2012-01-01

Febrile illnesses remain a major cause of morbidity and mortality in resource-poor countries, but too often, tests are not available to determine the causes, leading to misdiagnosis and inappropriate treatment. To determine the cause of febrile illnesses, we recovered the malaria smears from 102 children presenting with fever to Soddo Christian Hospital in Wolaitta Soddo, Ethiopia. DNA was isolated from the smears and evaluated by real-time polymerase chain reaction. We identified pathogen DNA with probes for Plasmodium spp., Streptococcus pneumoniae, Rickettsia spp., Salmonella spp., and Borrelia spp. Overall, we showed that it is possible to isolate high-quality DNA and identify treatable pathogens from malaria blood smears. Furthermore, our data showed that bacterial pathogens (especially Pneumococcus, Rickettsia spp., and Borrelia spp.) are common and frequently unrecognized but treatable causes of febrile illnesses in Ethiopian children. PMID:22764303

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482 T, isolated from raw cow milk

DOE PAGES

Laviad-Shitrit, Sivan; Göker, Markus; Huntemann, Marcel; ...

2017-05-08

Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome ismore » part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482 T, isolated from raw cow milk

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laviad-Shitrit, Sivan; Göker, Markus; Huntemann, Marcel

Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome ismore » part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

Hydroxybenzoic Acids Are Significant Contributors to the Antioxidant Effect of Borututu Bark, Cochlospermum angolensis Welw. ex Oliv.

PubMed Central

Abourashed, Ehab A.; Fu, Hao Wen

2017-01-01

Borututu (Cochlospermum angolensis) is an African tree whose bark has recently emerged as a herbal dietary supplement with claims for antioxidant activity. In order to substantiate the claimed activity of borututu supplements, we performed an activity-guided fractionation of the total extract utilizing a 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assay. Subsequent flash and centrifugal chromatography resulted in the isolation of gallic acid (1) and protocatechuic acid (2) as the main antioxidant constituents. Two apocarotenoids and one flavonoid were also isolated from the chloroform fraction and were identified as cochloxanthin (3), dihydrocochloxanthin (4), and 7,4′-dimethyltaxifolin (5), respectively. A High-performance liquid chromatography (HPLC) method was also developed for fingerprinting borututu samples, with Compounds 1–4 suggested as chemical markers for quality control purposes. PMID:28134834

Validation of a for anaerobic bacteria optimized MALDI-TOF MS biotyper database: The ENRIA project.

PubMed

Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Kostrzewa, M; Friedrich, A W

2018-03-12

Within the ENRIA project, several 'expertise laboratories' collaborated in order to optimize the identification of clinical anaerobic isolates by using a widely available platform, the Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Main Spectral Profiles (MSPs) of well characterized anaerobic strains were added to one of the latest updates of the Biotyper database db6903; (V6 database) for common use. MSPs of anaerobic strains nominated for addition to the Biotyper database are included in this validation. In this study, we validated the optimized database (db5989 [V5 database] + ENRIA MSPs) using 6309 anaerobic isolates. Using the V5 database 71.1% of the isolates could be identified with high confidence, 16.9% with low confidence and 12.0% could not be identified. Including the MSPs added to the V6 database and all MSPs created within the ENRIA project, the amount of strains identified with high confidence increased to 74.8% and 79.2%, respectively. Strains that could not be identified using MALDI-TOF MS decreased to 10.4% and 7.3%, respectively. The observed increase in high confidence identifications differed per genus. For Bilophila wadsworthia, Prevotella spp., gram-positive anaerobic cocci and other less commonly encountered species more strains were identified with higher confidence. A subset of the non-identified strains (42.1%) were identified using 16S rDNA gene sequencing. The obtained identities demonstrated that strains could not be identified either due to the generation of spectra of insufficient quality or due to the fact that no MSP of the encountered species was present in the database. Undoubtedly, the ENRIA project has successfully increased the number of anaerobic isolates that can be identified with high confidence. We therefore recommend further expansion of the database to include less frequently isolated species as this would also allow us to gain valuable insight into the clinical relevance of these less common anaerobic bacteria. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Quality of life, self-esteem and psychosocial factors in adolescents with acne vulgaris*

PubMed Central

Vilar, Gustavo Nunes; dos Santos, Laís Araújo; Sobral Filho, Jader Freire

2015-01-01

Background Dermatological diseases, among which acne vulgaris, have psychological impact on the affected generating feelings of guilt, shame and social isolation. Objectives To compare quality of life, self-esteem and other psychosocial variables amongst adolescents with and without acne vulgaris, and between levels of severity. Methods Cross-sectional observational study in a sample of 355 high school students from the city of João Pessoa. Data collection was performed with questionnaires and clinical-dermatological evaluation. The primary variables were the incidence of AV; quality of life, set by the Children's Dermatology Quality of Life Index and Dermatology Quality of Life Index; and self-esteem, measured by the Rosenberg Self-Esteem Scale. For calculation of statistical tests, we used the SPSS 20.0 software, considering p=0.05. Results The sample, with an average age of 16, showed 89.3% prevalence of acne vulgaris. The most prevalent psychosocial issue was "afraid that acne will never cease", present in 58% of affected youth. The median score of Quality of Life in Children's Dermatology Index was different amongst students with and without acne vulgaris (p=0.003), as well as the Quality of Life in Dermatology (p=0.038) scores, so that students with acne vulgaris have worse QoL. There was a correlation between the severity of acne vulgaris and worse quality of life. Self-esteem was not significantly associated with the occurrence or severity of acne vulgaris. Conclusions acne vulgaris assumes significance in view of its high prevalence and the effect on quality of life of adolescents, more severe at the more pronounced stages of disease (p<0.001). The psychosocial impact of acne vulgaris should be valued in the management of patients with this condition. PMID:26560206

Quality of life, self-esteem and psychosocial factors in adolescents with acne vulgaris.

PubMed

Vilar, Gustavo Nunes; Santos, Laís Araújo dos; Sobral Filho, Jader Freire

2015-01-01

Dermatological diseases, among which acne vulgaris, have psychological impact on the affected generating feelings of guilt, shame and social isolation. To compare quality of life, self-esteem and other psychosocial variables amongst adolescents with and without acne vulgaris, and between levels of severity. Cross-sectional observational study in a sample of 355 high school students from the city of João Pessoa. Data collection was performed with questionnaires and clinical-dermatological evaluation. The primary variables were the incidence of AV; quality of life, set by the Children's Dermatology Quality of Life Index and Dermatology Quality of Life Index; and self-esteem, measured by the Rosenberg Self-Esteem Scale. For calculation of statistical tests, we used the SPSS 20.0 software, considering p=0.05. The sample, with an average age of 16, showed 89.3% prevalence of acne vulgaris. The most prevalent psychosocial issue was "afraid that acne will never cease", present in 58% of affected youth. The median score of Quality of Life in Children's Dermatology Index was different amongst students with and without acne vulgaris (p=0.003), as well as the Quality of Life in Dermatology (p=0.038) scores, so that students with acne vulgaris have worse QoL. There was a correlation between the severity of acne vulgaris and worse quality of life. Self-esteem was not significantly associated with the occurrence or severity of acne vulgaris. acne vulgaris assumes significance in view of its high prevalence and the effect on quality of life of adolescents, more severe at the more pronounced stages of disease (p<0.001). The psychosocial impact of acne vulgaris should be valued in the management of patients with this condition.

Microbiological assessment of indoor air of a teaching hospital in Nigeria.

PubMed

Awosika, S A; Olajubu, F A; Amusa, N A

2012-06-01

To investigate the quality of indoor air of different wards and units of Olabisi Onabanjo University Teaching Hospital, Sagamu, to ascertain their contribution to infection rate in the hospital. The microbial quality of indoor air of nine wards/units of Olabisi Onabanjo University Teaching Hospital, Sagamu, Nigeria was conducted. Sedimentation technique using open Petri-dishes containing different culture media was employed and samplings were done twice daily, one in the morning shortly after cleaning and before influx of people/patients into the wards/units and the other in the evening when a lot of activities would have taken place in these wards. Isolates were identified according to standard methods. Results showed that there was a statistically significant difference (χ(2) = 6.016 7) in the bacteria population of the different sampling time whereas it was not so for fungi population (χ(2) = 0.285 7). Male medical ward (MMW) and male surgical general (MSG) recorded the highest bacterial and fungal growth while the operating theatre (OT) was almost free of microbial burden. The bacteria isolates were Staphylococcus aureus, Klebsiella sp., Bacillus cereus, Bacillus subtilis, Streptococcus pyogenes and Serratia marscences while the fungi isolates included Aspergillus flavus, Penicillium sp., Fusarium sp., Candida albicans and Alternaria sp. Staphylococcus aureus was the predominantly isolated bacterium while Penicillium sp. was the most isolated fungus. Though most of the microbial isolates were potential and or opportunistic pathogens, there was no correlation between the isolates in this study and the surveillance report of nosocomial infection during the period of study, hence the contribution of the indoor air cannot be established. From the reduction noticed in the morning samples, stringent measures such as proper disinfection and regular cleaning, restriction of patient relatives' movement in and out of the wards/units need to be enforced so as to improve the quality of indoor air of our hospital wards/units.

Exploration of indigenous bacteria in an intensive aquaculture system of African catfish (Clarias sp.) in Banyuwangi, Indonesia

NASA Astrophysics Data System (ADS)

Prayogo; Rahardja, B. S.; Asshanti, A. N.; Dewi, N. N.; Santanumurti, M. B.

2018-04-01

Intensive African catfish culture in tarpaulin pond was popular in Banyuwangi, Indonesia since the government supported the fisheries sector. Unfortunately, the failure of African catfish culture still occurred since the waste from fish metabolite process and feed residue decreased the water quality. Bacteria in the water could be the solution to increase the success rate of aquaculture by improving the water quality. This study purpose was to obtained indigenous bacteria in intensive aquaculture system of African catfish to improve water quality. This study successfully isolated bacteria contained with amylase, protease and lipase characteristic. Isolated bacteria in this study were identified as Pseudomonas pseudomallei (97.81%), Bacillus subtilis (95.81%) and Pseudomonas stutzeri (61.21%).

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

PubMed Central

Cooper, Vaughn S.; Hatcher, Philip J.; Verheyde, Bart; Carlier, Aurélien; Vandamme, Peter

2017-01-01

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence. PMID:28430818

Effect of vertical active vibration isolation on tracking performance and on ride qualities

NASA Technical Reports Server (NTRS)

Dimasi, F. P.; Allen, R. E.; Calcaterra, P. C.

1972-01-01

An investigation to determine the effect on pilot performance and comfort of an active vibration isolation system for a commercial transport pilot seat is reported. The test setup consisted of: a hydraulic shaker which produced random vertical vibration inputs; the active vibration isolation system; the pilot seat; the pilot control wheel and column; the side-arm controller; and a two-axis compensatory tracking task. The effects of various degrees of pilot isolation on short-term (two-minute) tracking performance and comfort were determined.

An efficient protocol for tissue sampling and DNA isolation from the stem bark of Leguminosae trees.

PubMed

Novaes, R M L; Rodrigues, J G; Lovato, M B

2009-02-03

Traditionally, molecular studies of plant species have used leaves as the source of DNA. However, sampling leaves from tall tree species can be quite difficult and expensive. We developed a sequence of procedures for using stem bark as a source of DNA from Leguminosae trees of the Atlantic Forest and the Cerrado. Leguminosae is an important species-rich family in these two highly diverse and endangered biomes. A modified CTAB protocol for DNA isolation is described, and details of the procedures for sampling and storage of the bark are given. The procedures were initially developed for three species, and then their applicability for 15 other species was evaluated. DNA of satisfactory quality was obtained from the bark of all species. The amounts of DNA obtained from leaves were slightly higher than from bark samples, while its purity was the same. Storing the bark frozen or by drying in silica gel yielded similar results. Polymerase chain reaction amplification worked for both plastid and nuclear genomes. This alternative for isolating DNA from bark samples of trees facilitates field work with these tree species.

High-quality draft genome sequence of Gracilimonas tropica CL-CB462 T (DSM 19535 T), isolated from a Synechococcus culture

DOE PAGES

Choi, Dong Han; Ahn, Chisang; Jang, Gwang Il; ...

2015-11-11

Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535 T, was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535 T was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project.more » Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. Finally, the strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535 T did not form spore.« less

Intermittent aortic cross-clamping for isolated CABG can save lives and money: experience with 15307 patients.

PubMed

Boethig, D; Minami, K; Lueth, J-U; El-Banayosy, A; Breymann, T; Koerfer, R

2004-06-01

The ideal myocardial protection during isolated CABG is still a matter of debate. Cardioplegia versus intermittent aortic cross-clamping (IACC) are the main opponents; the following article shows that IACC can be safe, efficient and might be cheaper than cardioplegia. Demographics and co-morbidities of 15307 CABG only patients consecutively operated on between January 1993 and October 2001 in the Heart Center in Bad Oeynhausen were assessed by the German Quality Assurance data set and risk-stratified using the EuroSCORE. Outcome (30-day or in-hospital mortality) was compared to the expected EuroSCORE estimation. Expected mortality was 3.25 %, observed mortality was 1.3 %, being significantly lower in the low, medium as well as high risk patients subgroup. Complication rates increased steadily with expected mortality rates. Stroke and myocardial infarction rates for patients with peripheral vessel disease were not higher than in comparable studies. More than 1000000 EUR were saved by lower cardioplegia bills. Myocardial protection with intermittent aortic cross-clamping for isolated CABG can be safe, effective, and economically advantageous when compared to cardioplegic solutions.

Isolation and screening of heterocystous cyanobacterial strains for biodiesel production by evaluating the fuel properties from fatty acid methyl ester (FAME) profiles.

PubMed

Anahas, Antonyraj Matharasi Perianaika; Muralitharan, Gangatharan

2015-05-01

This study reports on the biodiesel quality parameters of eleven heterocystous cyanobacterial strains based on fatty acid methyl esters (FAME) profiles. The biomass productivity of the tested cyanobacterial strains ranged from 9.33 to 20.67 mg L(-1) d(-1) while the lipid productivity varied between 0.65 and 2.358 mg L(-1) d(-1). The highest biomass and lipid productivity was observed for Calothrix sp. MBDU 013 but its lipid content is only 11.221 in terms of percent dry weight, next to the Anabaena sphaerica MBDU 105, whose lipid content is high. To identify the most competent isolate, a multi-criteria decision analyses (MCDA) was performed by including the key chemical and physical parameters of biodiesel calculated from FAME profiles. The isolate A.sphaerica MBDU 105 is the most promising biodiesel feed stock based on decision vector through Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA) analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improving the yield and quality of DNA isolated from white-rot fungi.

PubMed

Kuhad, R C; Kapoor, R K; Lal, R

2004-01-01

A new simple method used to eliminate polysaccharides that cause problems during DNA isolation was established for 6 different white-rot fungi using 1% hexadecyltrimethylammonium bromide (CTAB) as wash buffer and followed by centrifugation. Variation in the DNA yield and quality was ascertained using precipitating agents, detergents and cell-wall-hydrolyzing chitinase. Considerable amount of exopolysaccharides from fungal biomass was removed with the use of 1% CTAB wash buffer followed by centrifugation. The DNA varied in terms of yield and quality. For the DNA extraction use of 2% SDS in extraction buffer worked best for Pycnoporus cinnabarinus, Cyathus bulleri, Cyathus striatus and Cyathus stercoreus, while 2% CTAB worked best for Phanerochaete chrysosporium and Pleurotus ostreatus. Elimination of phenol and use of absolute ethanol for precipitating DNA resulted in good yield and quality of DNA. This DNA was amenable to restriction endonuclease digestion.

Mapping isolated wetlands with GIS and remote sensing in North Central Florida, USA

EPA Science Inventory

Wetlands perform many functions on the landscape related to water quality and quantity, and provide habitat for myriad organisms. The identification of wetlands can be problematic, especially in areas with numerous isolated wetlands, in mixed landuse areas, or over large geograph...

What do you think of my picture? Investigating factors of influence in profile images context perception

NASA Astrophysics Data System (ADS)

Mazza, F.; Da Silva, M. P.; Le Callet, P.; Heynderickx, I. E. J.

2015-03-01

Multimedia quality assessment has been an important research topic during the last decades. The original focus on artifact visibility has been extended during the years to aspects as image aesthetics, interestingness and memorability. More recently, Fedorovskaya proposed the concept of 'image psychology': this concept focuses on additional quality dimensions related to human content processing. While these additional dimensions are very valuable in understanding preferences, it is very hard to define, isolate and measure their effect on quality. In this paper we continue our research on face pictures investigating which image factors influence context perception. We collected perceived fit of a set of images to various content categories. These categories were selected based on current typologies in social networks. Logistic regression was adopted to model category fit based on images features. In this model we used both low level and high level features, the latter focusing on complex features related to image content. In order to extract these high level features, we relied on crowdsourcing, since computer vision algorithms are not yet sufficiently accurate for the features we needed. Our results underline the importance of some high level content features, e.g. the dress of the portrayed person and scene setting, in categorizing image.

Microbial quality of water in dental unit waterlines.

PubMed

Nikaeen, Mahnaz; Hatamzadeh, Maryam; Sabzevari, Zohre; Zareh, Omolbanin

2009-09-01

Dental unit waterlines (DUWLs) are ideal environment for development of microbial biofilms. Microbial contamination of water in DUWLs is thought to be the result of biofilm formation as it could serves as a haven for pathogens. The aim of this study was to assess microbial quality of water in dental unit waterlines of dental units located at the dental school of Isfahan University of Medical Sciences. Water samples were collected from air/water syringe and high-speed handpiece. Generally, 100-200 ml water samples were collected aseptically in sterile containers with sodium thiosulfate at the beginning of the day after a 2 minute purge. Samples were transferred to the laboratory in insulated box with cooling packs and examined for total viable heterotrophic bacteria and fungi. The heterotrophic plate count levels were significantly exceeded the American Dental Association recommendations for DUWL water quality (< 200 CFU/ml), in both air/water syringe (84%, CFU/ml: 500-20000) and high-speed handpiece (96%, CFU/ml: 710-36800) samples. However, there was no significant difference between the level of contamination in the air/water syringe and high-speed handpiece. Fungi were found in 28% and 36% of air/water syringe and high-speed handpiece samples, respectively; and filamentous fungi were the most frequently isolated fungi. DUWLs should be subjected to routine microbial monitoring and to a decontamination protocol in order to minimize the risk of exposure to potential pathogens from dental units.

The microbiological quality of ready-to-eat salads in Turkey: a focus on Salmonella spp. and Listeria monocytogenes.

PubMed

Gurler, Zeki; Pamuk, Sebnem; Yildirim, Yeliz; Ertas, Nurhan

2015-03-02

The microbiological safety of ready-to-eat (RTE) foods is of special concern as they are not exposed to further processing before consumption. In the present study, Listeria monocytogenes and Salmonella spp. were isolated from 15(6%) and 21(8%) samples respectively out of 261 RTE foods commercialized in Turkey. Escherichia coli was present in 10(4%) samples analyzed. Psychrotrophic aerobic populations >6logCFU/g were found in 36 (14%) of the samples, while total coliforms were detected in 155 (59%) of samples analyzed. All of the Salmonella spp. and L. monocytogenes isolates tested, exhibited resistance to one or more antimicrobial agents used. For Salmonella spp. isolates, resistance to penicillin (69%), erythromycin (38%), gentamicin (36%), tetracycline (36%) neomycin (33%), ampicillin (33%), amikacin (33%), vancomycin (33%), streptomycin (29%) cefotaxime (9%) and oxacillin (9%) was observed. For L. monocytogenes isolates, resistance to erythromycin (23%) and cephalothin (20%) was evident. The presence of pathogens and the relatively high resistance among the bacteria tested in RTE foods could pose public health and therapeutic problems in consumers. These results indicate the need of implementing hygienic rules in the production chain of RTE foods to ensure microbiological safety and to improve shelf life. Copyright © 2014 Elsevier B.V. All rights reserved.

Application of MALDI-TOF MS Systems in the Rapid Identification of Campylobacter spp. of Public Health Importance.

PubMed

Hsieh, Ying-Hsin; Wang, Yun F; Moura, Hercules; Miranda, Nancy; Simpson, Steven; Gowrishankar, Ramnath; Barr, John; Kerdahi, Khalil; Sulaiman, Irshad M

2018-05-01

Campylobacteriosis is an infectious gastrointestinal disease caused by Campylobacter spp. In most cases, it is either underdiagnosed or underreported due to poor diagnostics and limited databases. Several DNA-based molecular diagnostic techniques, including 16S ribosomal RNA (rRNA) sequence typing, have been widely used in the species identification of Campylobacter. Nevertheless, these assays are time-consuming and require a high quality of bacterial DNA. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS is an emerging diagnostic technology that can provide the rapid identification of microorganisms by using their intact cells without extraction or purification. In this study, we analyzed 24 American Type Culture Collection reference isolates of 16 Campylobacter spp. and five unknown clinical bacterial isolates for rapid identification utilizing two commercially available MADI-TOF MS platforms, namely the bioMérieux VITEK® MS and Bruker Biotyper systems. In addition, 16S rRNA sequencing was performed to confirm the species-level identification of the unknown clinical isolates. Both MALDI-TOF MS systems identified the isolates of C. jejuni, C. coli, C. lari, and C. fetus. The results of this study suggest that the MALDI-TOF MS technique can be used in the identification of Campylobacter spp. of public health importance.

Laser capture microdissection tailored to type 1 diabetes mellitus research.

PubMed

Szulawski, Robert; Nakazawa, Masato; McCall, Kelly D; James, Calvin B L; Schwartz, Frank L

2016-01-01

RNA isolation from pancreatic islets poses unique challenges. Here, we present a reproducible means of obtaining high-quality RNA from juvenile rodent islets in sufficient quantities for use in ex vivo expression studies. Tissue was extracted from female non-obese diabetic (NOD) toll-like receptor 3 (TLR3)(+/+) and (TLR3)(-/-) mice in the pre-diabetic stage. Samples were frozen in liquid nitrogen, sectioned, fixed in a highly alcoholic solution, and stained with an alcoholic cresyl violet (CV) solution. Rehydration of the fixed sections was minimized. Islets were identified visually and isolated with the Leica LMD6000 laser capture microdissection (LCM) system to yield samples highly enriched in islet RNA. Real time qPCR was performed on the islet cDNA using probes for CXC chemokine ligand 10 (CXCL10), an inflammatory marker that plays a critical role in the pathogenesis of type 1 diabetes mellitus (TIDM). This method represents an improvement over currently described LCM techniques for rodent pancreatic islets and makes feasible expression studies using small amounts of starting tissue without the need for RNA pre-amplification. This has immediate implications for ongoing TIDM studies using the NOD mouse.

Two Novel Anoxia-Induced Ethylene Response Factors That Interact with Promoters of Deastringency-Related Genes from Persimmon

PubMed Central

Min, Ting; Fang, Fang; Ge, Hang; Shi, Yan-na; Luo, Zheng-rong; Yao, Yun-cong; Grierson, Donald; Yin, Xue-ren; Chen, Kun-song

2014-01-01

A hypoxic environment is generally undesirable for most plants and stimulates anaerobic metabolism. It is a beneficial treatment, however, for the removal of astringency from persimmon to improve the fruit quality after harvest. High soluble tannins (SCTs) content is one of most important causes of astringency. High CO2 (95%) treatment effectively reduced SCTs in both “Mopan” and “Gongcheng-shuishi” persimmon fruit by causing increases in acetaldehyde. Using RNA-seq and realtime PCR, twelve ethylene response factor genes (DkERF11-22) were isolated and characterized, to determine those responsive to high CO2 treatment. Only two genes, DkERF19 and DkERF22, showed trans-activation effects on the promoters of deastringency-related genes pyruvate decarboxylase genes (DkPDC2 and DkPDC3) and the transcript levels of these genes was enhanced by hypoxia. Moreover, DkERF19 and the previously isolated DkERF9 had additive effects on activating the DkPDC2 promoter. Taken together, these results provide further evidence that transcriptome changes in the level of DkERF mRNAs regulate deastringency-related genes and their role in the mechanism of persimmon fruit deastringency is discussed. PMID:24805136

Evaluation of preservative efficacy in pharmaceutical products: the use of psychrotolerant, low-nutrient preferring microbes in challenge tests.

PubMed

Charnock, C; Otterholt, E

2012-10-01

Preservative efficacy in medicines is typically investigated using challenge tests. In such tests, the product is artificially contaminated with a high concentration of standard bacterial and fungal test strains such as Pseudomonas aeruginosa and Candida albicans. The rate and extent of reductions in inoculum viability over a specified period forms the basis for acceptance/rejection of preservative efficacy. None of the strains named for inclusion in the challenge test outlined in the European Pharmacopoeia are associated with the contamination of high-quality water used in pharmaceutical production. Alpha- and Betaproteobacteria are easily the most common microbes in waters intended for pharmaceutical production. In addition, none of the standard test strain panel prefer low-nutrient, dilute conditions or grow at or around refrigeration temperatures. This is important because the water activity and nutrient content of medicines can vary greatly and medicines are often stored cold. We investigate the relevance of these factors when testing preservative efficacy by including other strains in challenge tests. Psychrotolerant, low-nutrient preferring strains (Beta- and Alphaproteobacteria and a yeast) were isolated from pristine waters. These were compared in challenge tests with C. albicans and P. aeruginosa using different storage temperatures. Pharmaceutical products differing widely in water-content, pH and preservative systems were included in the study. Regardless of the type of medicine tested C. albicans always showed superior survival characteristics to the yeast isolate (Cryptococcus terricola). One of the three screened bacterial strains (a Sphingomonas sp.) survived significantly better than P. aeruginosa in all but one product tested. However, the results for all products taken together cannot easily be explained by reference to this strain's psychrotolerancy or its preference for dilute, low-nutrient environments. This study supports previous work indicating that the inclusion of wild-type test strains, in this instance strains that are suited to survival in high-quality waters, improves preservative efficacy tests. Use of a Sphingomonas sp. isolated from a pristine water as a challenge test strain, gave a more stringent indication of preservative efficacy in a wide range of pharmaceuticals than did P. aeruginosa. © 2012 Blackwell Publishing Ltd.

Establishment of a protocol for the gene expression analysis of laser microdissected rat kidney samples with affymetrix genechips

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stemmer, Kerstin; Ellinger-Ziegelbauer, Heidrun; Lotz, Kerstin

2006-11-15

Laser microdissection in conjunction with microarray technology allows selective isolation and analysis of specific cell populations, e.g., preneoplastic renal lesions. To date, only limited information is available on sample preparation and preservation techniques that result in both optimal histomorphological preservation of sections and high-quality RNA for microarray analysis. Furthermore, amplification of minute amounts of RNA from microdissected renal samples allowing analysis with genechips has only scantily been addressed to date. The objective of this study was therefore to establish a reliable and reproducible protocol for laser microdissection in conjunction with microarray technology using kidney tissue from Eker rats p.o. treatedmore » for 7 days and 6 months with 10 and 1 mg Aristolochic acid/kg bw, respectively. Kidney tissues were preserved in RNAlater or snap frozen. Cryosections were cut and stained with either H and E or cresyl violet for subsequent morphological and RNA quality assessment and laser microdissection. RNA quality was comparable in snap frozen and RNAlater-preserved samples, however, the histomorphological preservation of renal sections was much better following cryopreservation. Moreover, the different staining techniques in combination with sample processing time at room temperature can have an influence on RNA quality. Different RNA amplification protocols were shown to have an impact on gene expression profiles as demonstrated with Affymetrix Rat Genome 230{sub 2}.0 arrays. Considering all the parameters analyzed in this study, a protocol for RNA isolation from laser microdissected samples with subsequent Affymetrix chip hybridization was established that was also successfully applied to preneoplastic lesions laser microdissected from Aristolochic acid-treated rats.« less

Chronic social isolation enhances reproduction in the monogamous prairie vole (Microtus ochrogaster).

PubMed

Perry, Adam N; Carter, C Sue; Cushing, Bruce S

2016-06-01

Chronic stressors are generally considered to disrupt reproduction and inhibit mating. Here we test the hypothesis that a chronic stressor, specifically social isolation, can facilitate adaptive changes that enhance/accelerate reproductive effort. In general, monogamous species display high levels of prosociality, delayed sexual maturation, and greater parental investment in fewer, higher quality offspring compared with closely related polygynous species. We predicted that chronic social isolation would promote behavioral and neurochemical patterns in prairie voles associated with polygyny. Male and female prairie voles were isolated for four weeks and changes in mating behavior, alloparental care, estrogen receptor (ER) α expression and tyrosine hydroxylase (TH) expression in brain regions regulating sociosexual behavior were examined. In males, isolation accelerated copulation, increased ERα in the medial amygdala (MEApd) and bed nucleus of the stria terminalis (BSTpm), and reduced TH expression in the MEApd and BSTpm, but had no effect on alloparental behavior. In females, isolation resulted in more rapid estrus induction and reduced TH expression in the MEApd and BSTpm, but had no effect on estradiol sensitivity or ERα expression. The results support the hypothesis that ERα expression in the MEApd and BSTpm is a critical determinant of male copulatory behavior and/or mating system. The lack of change in alloparental behavior suggests that changes in prosocial behavior are selective and regulated by different mechanisms. The results also suggest that TH in the MEApd and BSTpm may play a critical role in determining mating behavior in both sexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolving Prehospital, Emergency Department, and “Inpatient” Management Models for Geriatric Emergencies

PubMed Central

Carpenter, Christopher R.; Platts-Mills, Timothy F.

2013-01-01

Alternative management methods are essential to ensure high quality and efficient emergency care for the growing number of geriatric adults worldwide. Protocols for case-finding and rapid diagnosis to support early condition-specific treatment for older adults with acute severe illness and injury are needed. Improved emergency department care for older adults will require providers to look beyond the diagnosis to address the influence of other factors on the patient's health: isolation and depression; finances and transportation; and chronic medical conditions and polypharmacy. This review article describes recent and ongoing efforts to enhance the quality of emergency care for older adults using alternative management approaches spanning the spectrum from prehospital care, through the emergency department, and into evolving inpatient or outpatient processes of care. PMID:23177599

A two-step electrodialysis method for DNA purification from polluted metallic environmental samples.

PubMed

Rodríguez-Mejía, José Luis; Martínez-Anaya, Claudia; Folch-Mallol, Jorge Luis; Dantán-González, Edgar

2008-08-01

Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.

Optimization of conditions for isolation of high quality chitin from shrimp processing raw byproducts using response surface methodology and its characterization.

PubMed

Nidheesh, T; Suresh, P V

2015-06-01

Chitin is one of the most abundant bioactive biopolymer on earth. It is commercially extracted from seafood processing crustacean shell byproducts by harsh thermochemical treatments. The extraction conditions, the source and pretreatment of raw material significantly affect its quality and bioactivity. In this investigation response surface methodology (RSM) has been applied to optimize and evaluate the interaction of variables for extraction of high quality chitin from shrimp processing raw byproducts. Variables such as, concentration of HCl (%, v/v) 4.5 (for wet) and 4.9 (for dry), reaction time 3 h, solid liquid ratio of HCl (w/v) 1:5.5 (for wet) and 1:7.9 (for dry) with two treatments achieved >98 % demineralization of shrimp byproduct. Variables such as, concentration of NaOH 3.6 % (w/v), reaction time 2.5 h, temperature 69.0 ± 1 °C, solid liquid ratio of NaOH 7.4 (w/v) and two treatments accomplished >98 % deproteinization of demineralized byproducts. Significant (p ≤ 0.05-0.001) interactive effects were observed between different variables. Chitin obtained in these conditions had residual content (%, w/w) of ash <0.4 and protein <0.8 and the degree of N-acetylation was >93 % with purity of >98 %. In conclusion, the optimized conditions by RSM can be applied for large scale preparation of high quality chitin from raw shrimp byproduct.

Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments.

PubMed

Desai, Chirayu; Madamwar, Datta

2007-03-01

PCR inhibitor-free metagenomic DNA of high quality and high yield was extracted from highly polluted sediments using a simple remediation strategy of adsorption and ion-exchange chromatography. Extraction procedure was optimized with series of steps, which involved gentle mechanical lysis, treatment with powdered activated charcoal (PAC) and ion-exchange chromatography with amberlite resin. Quality of the extracted DNA for molecular diversity analysis was tested by amplifying bacterial 16S rDNA (16S rRNA gene) with eubacterial specific universal primers (8f and 1492r), cloning of the amplified 16S rDNA and ARDRA (amplified rDNA restriction analysis) of the 16S rDNA clones. The presence of discrete differences in ARDRA banding profiles provided evidence for expediency of the DNA extraction protocol in molecular diversity studies. A comparison of the optimized protocol with commercial Ultraclean Soil DNA isolation kit suggested that method described in this report would be more efficient in removing metallic and organic inhibitors, from polluted sediment samples.

High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mhamdi, Ridha; Ardley, Julie; Tian, Rui

We report that Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350more » protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

DOE PAGES

Mhamdi, Ridha; Ardley, Julie; Tian, Rui; ...

2015-07-02

We report that Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350more » protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

Water quality and antifungal susceptibility of opportunistic yeast pathogens from rivers.

PubMed

Monapathi, M E; Bezuidenhout, C C; Rhode, O H J

2017-03-01

Yeasts from water sources have been associated with diseases ranging from superficial mucosal infections to life threatening diseases. The aim of this study was to determine the water quality as well as diversity and antifungal susceptibility of yeasts from two rivers. Yeast levels and physico-chemical parameter data were analyzed by principal component analysis to determine correlations between physico-chemical data and yeast levels. Yeast morphotypes were identified by biochemical tests and 26S rRNA gene sequencing. Disk diffusion antifungal susceptibility tests were conducted. Physico-chemical parameters of the water were within target water quality range (TWQR) for livestock farming. For irrigational use, total dissolved solids and nitrates were not within the TWQR. Yeast levels ranged between 27 ± 10 and 2,573 ± 306 cfu/L. Only non-pigmented, ascomycetous yeasts were isolated. Saccharomyces cerevisiae and Candida glabrata were most frequently isolated. Several other opportunistic pathogens were also isolated. A large number of isolates were resistant to azoles, especially fluconazole, but also to other antifungal classes. Candida species were resistant to almost all the antifungal classes. These water sources are used for recreation and religious as well as for watering livestock and irrigation. Of particular concern is the direct contact of individuals with opportunistic yeast, especially the immune-compromised. Resistance of these yeast species to antifungal agents is a further health concern.

Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology

PubMed Central

2010-01-01

Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost of purchasing these kits over a long run can be considerable. Furthermore, a simple method for the isolation of binary plasmid from Agrobacterium tumefaciens cells with satisfactory yield is lacking. Here we describe an easy protocol using homemade silicon dioxide matrix and seven simple solutions for DNA extraction from E. coli and A. tumefaciens cells, PCR and restriction digests, agarose gel slices, and plant tissues. Compared with the commercial kits, this protocol allows rapid DNA purification from diverse sources with comparable yield and purity at negligible cost. Following this protocol, we have demonstrated: (1) DNA fragments as small as a MYC-epitope tag coding sequence can be successfully recovered from an agarose gel slice; (2) Miniprep DNA from E. coli can be eluted with as little as 5 μl water, leading to high DNA concentrations (>1 μg/μl) for efficient biolistic bombardment of Arabidopsis seedlings, polyethylene glycol (PEG)-mediated Arabidopsis protoplast transfection and maize protoplast electroporation; (3) Binary plasmid DNA prepared from A. tumefaciens is suitable for verification by restriction analysis without the need for large scale propagation; (4) High-quality genomic DNA is readily isolated from several plant species including Arabidopsis, tobacco and maize. Thus, the silicon dioxide matrix-based DNA purification protocol offers an easy, efficient and economical way to extract DNA for various purposes in plant research. PMID:20180960

[Influence of Cryopreservation on Human Peripheral Blood Mononuclear Cell Immunocompetence].

PubMed

Pan, Xue-Feng; Lu, Chun-Xia; Yang, Li-Li; Shu, Chang; Yao, Na; Zuo, Hong-Bin; Cui, Li-Feng

2016-08-01

To establish a method for isolation, cryopreservation and recovery of the highly viable human peripheral blood monomuclear cells (PBMNCs) so as to achieve the long-term preservation of PBMNCs. A total of 80-100 ml peripheral blood were collected from the healthy volumteers aged over 50 years old. The PBMNCs were isolated by the Ficoll density gradient technique and cryopreserved gradually by program control method in liquid nitrogen freezer of -196 °C. The serum-free medium and autoloqous plasma medium were test for preservation of PBMNCs. The cell viability was assessed at time point of 1, 2, 4, 8, 12 and 24 months after thawing. Finally, the proliferation ability, purity and cytotoxicity were compared between the autologous immune lymphocytes (AIL) induced from cryopreserved PBMNCs and AIL as control from fresh PBMNCs. After separating, the cell viability was 99.6%±0.4%, and the recovery rate of lymphocytes was 58.4%±6.52%. The cell recovery rate of lymphocyte was 89.7%±3.82% at 24 months. The quality assurance program was reliable within 2 years of running. The AIL cells induced with cryopreserved PBMNCs were not significantly different from those induced from fresh PBMNCs in terms of proliferative action, purity and cytotoxicity(CD3(+)CD8(+) ≥45%,CD3(+)CD56(+) NKT≥10%,CD4(+)CD25(+) NKT≤10%). Manual separation of lymphocytes in vitro can get enough high-quality PBMNCs. The long-term cryopreserved PBMNC still maintain their high viability. The reinfusion of the clinical autologous immune cells would be advantageous for early tumor immunotherapy. Human AIL induced from cryopreserved PBMNC maintain their anti-tumor ability. These findings have the important implications for the application of these cells to adoptive cellular therapy.

Resonant inelastic light scattering and photoluminescence in isolated nc-Si/SiO{sub 2} quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bairamov, F. B., E-mail: Bairamov@mail.ioffe.ru; Toporov, V. V.; Poloskin, E. D.

2013-05-15

Observation at the room temperature the spectra of the resonant inelastic light scattering by the spatially confined optical phonons as well as the excitonic luminescence caused by confinement effects in the ensemble of isolated quantum dots (QDs) nc-Si/SiO{sub 2} is reported. It is shown that the samples investigated are high purity and high crystalline perfection quality nc-Si/SiO{sub 2} QDs without amorphous phase {alpha}-Si and contaminants. Comparison between the experimental data obtained and phenomenological model of the strong space confinement of optical phonons revealed the need of the more accurate form of the weighted function for the confinement of optical phonons.more » It is shown that simultaneous detection of the inelastic light scattering by the confinement of phonons and the excitonic luminescence spectra by the confined electron-hole pairs in the nc-Si/SiO{sub 2} QDs allows selfconsistently to determine more accurate values of the diameter of the nc-Si/SiO{sub 2} QDs.« less

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

PubMed

Feehan, Joanna M; Scheibel, Katherine E; Bourras, Salim; Underwood, William; Keller, Beat; Somerville, Shauna C

2017-03-31

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

77 FR 6666 - Airworthiness Directives; CFM International, S.A. Turbofan Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-09

... International, S.A. model CFM56-5B series turbofan engines. This AD was prompted by a normal quality sampling at... quality sampling at CFM International. S.A. that isolated a production batch of fan blades with...

Allogeneic stem cell transplantation in children with acute lymphoblastic leukemia after isolated central nervous system relapse: our experiences and review of the literature.

PubMed

Yoshihara, T; Morimoto, A; Kuroda, H; Imamura, T; Ishida, H; Tsunamoto, K; Naya, M; Hibi, S; Todo, S; Imashuku, S

2006-01-01

The prognosis of patients with acute lymphoblastic leukemia (ALL) and central nervous system (CNS) relapse has historically been very poor. Although chemo-radiotherapy has improved outcomes, some patients still have a poor prognosis after CNS relapse. Therefore, allogeneic hematopoietic stem cell transplantation (allo-SCT) has recently become an option for treatment of CNS leukemia; however, information, particularly on the long-term outcome of transplant recipients, is limited. We performed allo-SCT in eight pediatric patients with ALL (n=7) or T-cell type non-Hodgkin's lymphoma (n=1), who had isolated CNS relapse. All patients survived for a median of 70.5 (range, 13-153) months after SCT. Sequelae developed late in some patients: mental retardation (IQ=47) in one patient, severe alopecia in two patients, limited chronic graft-versus-host-disease in three patients, and amenorrhea and/or hypothyroidism in three patients. Except for a pre-school child with post transplant CNS relapse, six out of seven patients show normal school/social performance. Our results clearly indicate a high cure rate of isolated CNS relapse by allo-SCT in pediatric lymphoid malignancies; however, there needs to be further studies to determine which are the appropriate candidates for transplantation and what is the best transplant regimen to achieve high cure rate and maintain good quality of life.

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE PAGES

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui; ...

2015-10-26

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE PAGES

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter; ...

2015-10-16

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Nanoliter reactors improve multiple displacement amplification of genomes from single cells.

PubMed

Marcy, Yann; Ishoey, Thomas; Lasken, Roger S; Stockwell, Timothy B; Walenz, Brian P; Halpern, Aaron L; Beeson, Karen Y; Goldberg, Susanne M D; Quake, Stephen R

2007-09-01

Since only a small fraction of environmental bacteria are amenable to laboratory culture, there is great interest in genomic sequencing directly from single cells. Sufficient DNA for sequencing can be obtained from one cell by the Multiple Displacement Amplification (MDA) method, thereby eliminating the need to develop culture methods. Here we used a microfluidic device to isolate individual Escherichia coli and amplify genomic DNA by MDA in 60-nl reactions. Our results confirm a report that reduced MDA reaction volume lowers nonspecific synthesis that can result from contaminant DNA templates and unfavourable interaction between primers. The quality of the genome amplification was assessed by qPCR and compared favourably to single-cell amplifications performed in standard 50-microl volumes. Amplification bias was greatly reduced in nanoliter volumes, thereby providing a more even representation of all sequences. Single-cell amplicons from both microliter and nanoliter volumes provided high-quality sequence data by high-throughput pyrosequencing, thereby demonstrating a straightforward route to sequencing genomes from single cells.

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome

PubMed Central

2013-01-01

Background Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species have been instrumental in showing the benefit of analyzing patterns of sequence conservation. Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate. Results Here, we report the genome sequence and analysis of Saccharomyces arboricolus, a yeast species recently isolated in China, that is closely related to S. cerevisiae. We obtained high quality de novo sequence and assemblies using a combination of next generation sequencing technologies, established the phylogenetic position of this species and considered its phenotypic profile under multiple environmental conditions in the light of its gene content and phylogeny. Conclusions We suggest that the genome of S. arboricolus will be useful in future comparative genomics analysis of the Saccharomyces sensu stricto yeasts. PMID:23368932

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Degradation of CMOS image sensors in deep-submicron technology due to γ-irradiation

NASA Astrophysics Data System (ADS)

Rao, Padmakumar R.; Wang, Xinyang; Theuwissen, Albert J. P.

2008-09-01

In this work, radiation induced damage mechanisms in deep submicron technology is resolved using finger gated-diodes (FGDs) as a radiation sensitive tool. It is found that these structures are simple yet efficient structures to resolve radiation induced damage in advanced CMOS processes. The degradation of the CMOS image sensors in deep-submicron technology due to γ-ray irradiation is studied by developing a model for the spectral response of the sensor and also by the dark-signal degradation as a function of STI (shallow-trench isolation) parameters. It is found that threshold shifts in the gate-oxide/silicon interface as well as minority carrier life-time variations in the silicon bulk are minimal. The top-layer material properties and the photodiode Si-SiO2 interface quality are degraded due to γ-ray irradiation. Results further suggest that p-well passivated structures are inevitable for radiation-hard designs. It was found that high electrical fields in submicron technologies pose a threat to high quality imaging in harsh environments.

Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology.

PubMed

Harper, Kathryn A; Meiklejohn, Kelly A; Merritt, Richard T; Walker, Jessica; Fisher, Constance L; Robertson, James M

2018-02-01

Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.

Recent Advances in Marine Algae Polysaccharides: Isolation, Structure, and Activities.

PubMed

Xu, Shu-Ying; Huang, Xuesong; Cheong, Kit-Leong

2017-12-13

Marine algae have attracted a great deal of interest as excellent sources of nutrients. Polysaccharides are the main components in marine algae, hence a great deal of attention has been directed at isolation and characterization of marine algae polysaccharides because of their numerous health benefits. In this review, extraction and purification approaches and chemico-physical properties of marine algae polysaccharides (MAPs) are summarized. The biological activities, which include immunomodulatory, antitumor, antiviral, antioxidant, and hypolipidemic, are also discussed. Additionally, structure-function relationships are analyzed and summarized. MAPs' biological activities are closely correlated with their monosaccharide composition, molecular weights, linkage types, and chain conformation. In order to promote further exploitation and utilization of polysaccharides from marine algae for functional food and pharmaceutical areas, high efficiency, and low-cost polysaccharide extraction and purification methods, quality control, structure-function activity relationships, and specific mechanisms of MAPs activation need to be extensively investigated.

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, Supratim; Lapidus, Alla; Shapiro, Nicole

2015-01-01

Pontibacter roseus Suresh et al 2006 is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50more » RNA genes and is a part of Genomic encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project.« less

A Strategy for Simultaneous Isolation of Less Polar Ginsenosides, Including a Pair of New 20-Methoxyl Isomers, from Flower Buds of Panax ginseng.

PubMed

Li, Sha-Sha; Li, Ke-Ke; Xu, Fei; Tao, Li; Yang, Li; Chen, Shu-Xiao; Gong, Xiao-Jie

2017-03-10

The present study was designed to simultaneously isolate the less polar ginsenosides from the flower buds of Panax ginseng (FBPG). Five ginsenosides, including a pair of new 20-methoxyl isomers, were extracted from FBPG and purified through a five-step integrated strategy, by combining ultrasonic extraction, Diaion Hp-20 macroporous resin column enrichment, solid phase extraction (SPE), reversed-phase high-performance liquid chromatography (RP-HPLC) analysis and preparation, and nuclear magnetic resonance (NMR) analysis. The quantification of the five ginsenosides was also discussed by a developed method with validations within acceptable limits. Ginsenoside Rg5 showed content of about 1% in FBPG. The results indicated that FBPG might have many different ginsenosides with diverse chemical structures, and the less polar ginsenosides were also important to the quality control and standardization of FBPG.

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

DOE PAGES

Mukherjee, Supratim; Lapidus, Alla; Shapiro, Nicole; ...

2015-02-09

Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1 T along with its complete genome sequence and annotation from a culture of DSM 17521 T. In conclusion, the 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50more » RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.« less

High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass

DOE PAGES

Laviad, Sivan; Lapidus, Alla; Han, James; ...

2015-05-27

Brachymonas chironomi strain AIMA4T (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4T in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. We find the DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins andmore » 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.« less

Optimal Sensor Allocation for Fault Detection and Isolation

NASA Technical Reports Server (NTRS)

Azam, Mohammad; Pattipati, Krishna; Patterson-Hine, Ann

2004-01-01

Automatic fault diagnostic schemes rely on various types of sensors (e.g., temperature, pressure, vibration, etc) to measure the system parameters. Efficacy of a diagnostic scheme is largely dependent on the amount and quality of information available from these sensors. The reliability of sensors, as well as the weight, volume, power, and cost constraints, often makes it impractical to monitor a large number of system parameters. An optimized sensor allocation that maximizes the fault diagnosibility, subject to specified weight, volume, power, and cost constraints is required. Use of optimal sensor allocation strategies during the design phase can ensure better diagnostics at a reduced cost for a system incorporating a high degree of built-in testing. In this paper, we propose an approach that employs multiple fault diagnosis (MFD) and optimization techniques for optimal sensor placement for fault detection and isolation (FDI) in complex systems. Keywords: sensor allocation, multiple fault diagnosis, Lagrangian relaxation, approximate belief revision, multidimensional knapsack problem.

Mixotrophic and heterotrophic production of lipids and carbohydrates by a locally isolated microalga using wastewater as a growth medium.

PubMed

Nzayisenga, Jean Claude; Eriksson, Karolina; Sellstedt, Anita

2018-06-01

The biomass production and changes in biochemical composition of a locally isolated microalga (Chlorella sp.) were investigated in autotrophic, mixotrophic and heterotrophic conditions, using glucose or glycerol as carbon sources and municipal wastewater as the growth medium. Both standard methods and Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) analysis of data acquired by Fourier-transform IR (FTIR) spectrometry showed that autotrophic and mixotrophic conditions promoted carbohydrate accumulation, while heterotrophic conditions with glycerol resulted in the highest lipid content and lowest carbohydrate content. Heterotrophic conditions with glycerol as a carbon source also resulted in high oleic acid (18:1) contents and low linolenic acid (18:3) contents, and thus increasing biodiesel quality. The results also show the utility of MCR-ALS for analyzing changes in microalgal biochemical composition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Compact photonic crystal circulator with flat-top transmission band created by cascading magneto-optical resonance cavities.

PubMed

Wang, Qiong; Ouyang, Zhengbiao; Lin, Mi; Liu, Qiang

2015-11-20

A new type of compact three-port circulator with flat-top transmission band (FTTB) in a two-dimensional photonic crystal has been proposed, through coupling the cascaded magneto-optical resonance cavities to waveguides. The coupled-mode theory is applied to investigate the coupled structure and analyze the condition to achieve FTTB. According to the theoretical analysis, the structure is further optimized to ensure that the condition for achieving FTTB can be satisfied for both cavity-cavity coupling and cavity-waveguide coupling. Through the finite-element method, it is demonstrated that the design can realize a high quality, nonreciprocal circulating propagation of waves with an insertion loss of 0.023 dB and an isolation of 23.3 dB, covering a wide range of operation frequency. Such a wideband circulator has potential applications in large-scale integrated photonic circuits for guiding or isolating harmful optical reflections from load elements.

Screening and identification of aerobic denitrifiers

NASA Astrophysics Data System (ADS)

Shao, K.; Deng, H. M.; Chen, Y. T.; Zhou, H. J.; Yan, G. X.

2016-08-01

With the standards of the effluent quality more stringent, it becomes a quite serious problem for municipalities and industries to remove nitrogen from wastewater. Bioremediation is a potential method for the removal of nitrogen and other pollutants because of its high efficiency and low cost. Seven predominant aerobic denitrifiers were screened and characterized from the activated sludge in the CAST unit. Some of these strains removed 87% nitrate nitrogen at least. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as the genera of Ralstonia, Achromobacter, Aeromonas and Enterobacter.

Real time workload classification from an ambulatory wireless EEG system using hybrid EEG electrodes.

PubMed

Matthews, R; Turner, P J; McDonald, N J; Ermolaev, K; Manus, T; Shelby, R A; Steindorf, M

2008-01-01

This paper describes a compact, lightweight and ultra-low power ambulatory wireless EEG system based upon QUASAR's innovative noninvasive bioelectric sensor technologies. The sensors operate through hair without skin preparation or conductive gels. Mechanical isolation built into the harness permits the recording of high quality EEG data during ambulation. Advanced algorithms developed for this system permit real time classification of workload during subject motion. Measurements made using the EEG system during ambulation are presented, including results for real time classification of subject workload.

Impaired performance from brief social isolation of rhesus monkeys (Macaca mulatta) - A multiple video-task assessment

NASA Technical Reports Server (NTRS)

Washburn, David A.; Rumbaugh, Duane M.

1991-01-01

Social isolation has been demonstrated to produce profound and lasting psychological effects in young primates. In the present investigation, two adult rhesus monkeys (Macaca mulatta) were isolated from one another for up to 6 days and tested on 7 video tasks designed to assess psychomotor and cognitive functioning. Both the number and quality (i.e., speed and accuracy) of responses were significantly compromised in the social isolation condition relative to levels in which the animals were tested together. It is argued that adult rhesus are susceptible to performance disruption by even relatively brief social isolation, and that these effects can best be assessed by a battery of complex and sensitive measures.

Phenetic, genetic diversity and symbiotic compatibility of rhizobial strains nodulating pigeon pea in Northern India.

PubMed

Arora, Naveen Kumar; Khare, Ekta; Singh, Sachin; Tewari, Sakshi

2018-01-01

Pigeon pea ( Cajanus cajan ) is one of the most important legumes grown in the northern province of Uttar Pradesh, India. However, its productively in Uttar Pradesh is lower than the average yield of adjoining states. During the course of the present study, a survey of pigeon pea growing agricultural fields was carried out and it was found that 80% of plants were inadequately nodulated. The study was aimed to evaluate the pigeon pea symbiotic compatibility and nodulation efficiency of root nodulating bacteria isolated from various legumes, and to explore the phenetic and genetic diversity of rhizobial population nodulating pigeon pea growing in fields of Uttar Pradesh. Amongst all the 96 isolates, 40 isolates showed nodulation in pigeon pea. These 40 isolates were further characterized by phenotypic, biochemical and physiological tests. Intrinsic antibiotic resistance pattern was taken to generate similarity matrix revealing 10 phenons. The study shows that most of the isolates nodulating pigeon pea in this region were rapid growers. The dendrogram generated using the NTSYSpc software grouped RAPD patterns into 19 clusters. The high degree of phenetic and genetic diversity encountered is probably because of a history of mixed cropping of legumes. The assessment of diversity is a very important tool and can be used to improve the nodulation and quality of pigeon pea crop. It is also concluded that difference between phenetic and RAPD clustering pattern is an indication that rhizobial diversity of pigeon pea is not as yet completely understood and settled.

Minor diterpene glycosides from the leaves of Stevia rebaudiana.

PubMed

Ibrahim, Mohamed A; Rodenburg, Douglas L; Alves, Kamilla; Fronczek, Frank R; McChesney, James D; Wu, Chongming; Nettles, Brian J; Venkataraman, Sylesh K; Jaksch, Frank

2014-05-23

Two new diterpene glycosides in addition to five known glycosides have been isolated from a commercial extract of the leaves of Stevia rebaudiana. Compound 1 (rebaudioside KA) was shown to be 13-[(O-β-d-glucopyranosyl)oxy]ent-kaur-16-en-19-oic acid 2-O-β-d-glucopyranosyl-β-d-glucopyranosyl ester and compound 2, 12-α-[(2-O-β-d-glucopyranosyl-β-d-glucopyranosyl)oxy]ent-kaur-16-en-19-oic acid β-d-glucopyranosyl ester. Five additional known compounds were identified, rebaudioside E, rebaudioside M, rebaudioside N, rebaudioside O, and stevioside, respectively. Enzymatic hydrolysis of stevioside afforded the known ent-kaurane aglycone 13-hydroxy-ent-kaur-16-en-19-oic acid (steviol) (3). The isolated metabolite 1 possesses the ent-kaurane aglycone steviol (3), while compound 2 represents the first example of the isomeric diterpene 12-α-hydroxy-ent-kaur-16-en-19-oic acid existing as a glycoside in S. rebaudiana. The structures of the isolated metabolites 1 and 2 were determined based on comprehensive 1D- and 2D-NMR (COSY, HSQC, and HMBC) studies. A high-quality crystal of compound 3 has formed, which allowed the acquisition of X-ray diffraction data that confirmed its structure. The structural similarities between the new metabolites and the commercially available stevioside sweeteners suggest the newly isolated metabolites should be examined for their organoleptic properties. Accordingly rebaudiosides E, M, N, O, and KA have been isolated in greater than gram quantities.

DNA and bone structure preservation in medieval human skeletons.

PubMed

Coulson-Thomas, Yvette M; Norton, Andrew L; Coulson-Thomas, Vivien J; Florencio-Silva, Rinaldo; Ali, Nadir; Elmrghni, Samir; Gil, Cristiane D; Sasso, Gisela R S; Dixon, Ronald A; Nader, Helena B

2015-06-01

Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Presence of multi-drug resistant pathogenic Escherichia coli in the San Pedro River located in the State of Aguascalientes, Mexico

PubMed Central

Ramírez Castillo, Flor Y.; Avelar González, Francisco J.; Garneau, Philippe; Márquez Díaz, Francisco; Guerrero Barrera, Alma L.; Harel, Josée

2013-01-01

Contamination of surface waters in developing countries is a great concern. Treated and untreated wastewaters have been discharged into rivers and streams, leading to possible waterborne infection outbreaks and may represent a significant dissemination mechanism of antibiotic resistance genes. In this study, the water quality of San Pedro River, the main river and pluvial collector of the Aguascalientes State, Mexico was assessed. Thirty sample locations were tested throughout the River. The main physicochemical parameters of water were evaluated. Results showed high levels of fecal pollution as well as inorganic and organic matter abundant enough to support the heterotrophic growth of microorganisms. These results indicate poor water quality in samples from different locations. One hundred and fifty Escherichia coli were collected and screened by PCR for several virulence genes. Isolates were classified as either pathogenic (n = 91) or commensal (n = 59). The disc diffusion method was used to determine antimicrobial susceptibility to 13 antibiotics. Fifty-two percent of the isolates were resistant to at least one antimicrobial agent and 30.6% were multi-resistant. Eighteen E. coli strains were quinolone resistant of which 16 were multi-resistant. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 12 isolates. Mutations at the Ser-83→Leu and/or Asp-87→Asn in the gyrA gene were detected as well as mutations at the Ser-80→Ile in parC. An E. coli microarray (Maxivirulence V 3.1) was used to characterize the virulence and antimicrobial resistance genes profiles of the fluoroquinolone-resistant isolates. Antimicrobial resistance genes such as blaTEM, sulI, sulII, dhfrIX, aph3 (strA), and tet (B) as well as integrons were found in fluoroquinolone (FQ) resistance E. coli strains. The presence of potential pathogenic E. coli and antibiotic resistance in San Pedro River such as FQ resistant E. coli could pose a potential threat to human and animal health. PMID:23785356

Featured Article: Isolation, characterization, and cultivation of human hepatocytes and non-parenchymal liver cells

PubMed Central

Pfeiffer, Elisa; Kegel, Victoria; Zeilinger, Katrin; Hengstler, Jan G; Nüssler, Andreas K; Seehofer, Daniel

2015-01-01

Primary human hepatocytes (PHH) are considered to be the gold standard for in vitro testing of xenobiotic metabolism and hepatotoxicity. However, PHH cultivation in 2D mono-cultures leads to dedifferentiation and a loss of function. It is well known that hepatic non-parenchymal cells (NPC), such as Kupffer cells (KC), liver endothelial cells (LEC), and hepatic stellate cells (HSC), play a central role in the maintenance of PHH functions. The aims of the present study were to establish a protocol for the simultaneous isolation of human PHH and NPC from the same tissue specimen and to test their suitability for in vitro co-culture. Human PHH and NPC were isolated from tissue obtained by partial liver resection by a two-step EDTA/collagenase perfusion technique. The obtained cell fractions were purified by Percoll density gradient centrifugation. KC, LEC, and HSC contained in the NPC fraction were separated using specific adherence properties and magnetic activated cell sorting (MACS®). Identified NPC revealed a yield of 1.9 × 106 KC, 2.7 × 105 LEC and 4.7 × 105 HSC per gram liver tissue, showing viabilities >90%. Characterization of these NPC showed that all populations went through an activation process, which influenced the cell fate. The activation of KC strongly depended on the tissue quality and donor anamnesis. KC became activated in culture in association with a loss of viability within 4–5 days. LEC lost specific features during culture, while HSC went through a transformation process into myofibroblasts. The testing of different culture conditions for HSC demonstrated that they can attenuate, but not prevent dedifferentiation in vitro. In conclusion, the method described allows the isolation and separation of PHH and NPC in high quality and quantity from the same donor. PMID:25394621

Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

PubMed Central

Peña-Llopis, Samuel; Brugarolas, James

2014-01-01

Genomic technologies have revolutionized our understanding of complex Mendelian diseases and cancer. Solid tumors present several challenges for genomic analyses, such as tumor heterogeneity and tumor contamination with surrounding stroma and infiltrating lymphocytes. We developed a protocol to (i) select tissues of high cellular purity on the basis of histological analyses of immediately flanking sections and (ii) simultaneously extract genomic DNA (gDNA), messenger RNA (mRNA), noncoding RNA (ncRNA; enriched in microRNA (miRNA)) and protein from the same tissues. After tissue selection, about 12–16 extractions of DNA/RNA/protein can be obtained per day. Compared with other similar approaches, this fast and reliable methodology allowed us to identify mutations in tumors with remarkable sensitivity and to perform integrative analyses of whole-genome and exome data sets, DNA copy numbers (by single-nucleotide polymorphism (SNP) arrays), gene expression data (by transcriptome profiling and quantitative PCR (qPCR)) and protein levels (by western blotting and immunohistochemical analysis) from the same samples. Although we focused on renal cell carcinoma, this protocol may be adapted with minor changes to any human or animal tissue to obtain high-quality and high-yield nucleic acids and proteins. PMID:24136348

High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

PubMed

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

2017-11-03

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

High Resolution Melting (HRM) for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

PubMed Central

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz

2017-01-01

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup. PMID:29099791

Improved RF Isolation Amplifier

NASA Technical Reports Server (NTRS)

Stevens, G. L.; Macconnell, J.

1985-01-01

Circuit has high reverse isolation and wide bandwidth. Wideband isolation amplifier has low intermodulation distortion and high reverse isolation. Circuit does not require selected or matched components or directional coupling device. Circuit used in applications requiring high reverse isolation such as receiver intermediate-frequency (IF) strips and frequency distribution systems. Also applicable in RF and video signaling.

Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin.

PubMed

Sadowy, Ewa; Luczkiewicz, Aneta

2014-03-14

Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred in a big part in a hospital environment, leading to formation of high-risk enterococcal clonal complexes (HiRECCs), which combine multidrug resistance with increased pathogenicity and epidemicity. The aim of this study was to establish the species composition in wastewater, its marine recipient as well as a river estuary and to investigate the antimicrobial susceptibility of collected isolates. Molecular methods were additionally applied to test the presence of HiRRECC-related E. faecium. Two wastewater treatment plants (WWTPs), their marine outfalls and Vistula river that influence significantly the quality of waters in Gulf of Gdansk were sampled to investigate the presence of Enterococcus spp. Four-hundred-twenty-eight isolates were obtained, including E. faecium (244 isolates, 57.0%), E. hirae (113 isolates, 26.4%) and E. faecalis (63 isolates, 14.7%); other species (E. gallinarum/casseliflavus, E. durans and E. avium) accounted for 1.9%. Antimicrobial susceptibility testing revealed the presence of isolates resistant to erythromycin, tetracycline, amipicillin, fluoroquinolones and aminoglycosides (high-level resistance), especially among E. faecium, where such isolates were usually characterized by multilocus sequence types associated with nosocomial lineages 17, 18 and 78 of this species representing HiRECC, formerly called CC17. These isolates not only carried several resistance determinants but were also enriched in genes encoding pathogenicity factors (Esp, pili) and genes associated with mobile genetic elements (MGE), a feature also typical for nosocomial HiRECC. Our data show that WWTPs constitute an important source of enterococcal strains carrying antimicrobial resistance determinants, often associated with the presence of MGE, for the recipient water environment, thus increasing a pool of such genes for other organisms. The presence of HiRECCs in wastewaters and marine/river environment may indicate that adaptations gained in hospitals may be also beneficial for survival of such clones in other settings. There is an obvious need to monitor the release and spread of such strains in order to elucidate better ways to curb their dissemination.

Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin

PubMed Central

2014-01-01

Background Enterococci, ubiquitous colonizers of humans and other animals, play an increasingly important role in health-care associated infections (HAIs). It is believed that the recent evolution of two clinically relevant species, Enterococcus faecalis and Enterococcus faecium occurred in a big part in a hospital environment, leading to formation of high-risk enterococcal clonal complexes (HiRECCs), which combine multidrug resistance with increased pathogenicity and epidemicity. The aim of this study was to establish the species composition in wastewater, its marine recipient as well as a river estuary and to investigate the antimicrobial susceptibility of collected isolates. Molecular methods were additionally applied to test the presence of HiRRECC-related E. faecium. Results Two wastewater treatment plants (WWTPs), their marine outfalls and Vistula river that influence significantly the quality of waters in Gulf of Gdansk were sampled to investigate the presence of Enterococcus spp. Four-hundred-twenty-eight isolates were obtained, including E. faecium (244 isolates, 57.0%), E. hirae (113 isolates, 26.4%) and E. faecalis (63 isolates, 14.7%); other species (E. gallinarum/casseliflavus, E. durans and E. avium) accounted for 1.9%. Antimicrobial susceptibility testing revealed the presence of isolates resistant to erythromycin, tetracycline, amipicillin, fluoroquinolones and aminoglycosides (high-level resistance), especially among E. faecium, where such isolates were usually characterized by multilocus sequence types associated with nosocomial lineages 17, 18 and 78 of this species representing HiRECC, formerly called CC17. These isolates not only carried several resistance determinants but were also enriched in genes encoding pathogenicity factors (Esp, pili) and genes associated with mobile genetic elements (MGE), a feature also typical for nosocomial HiRECC. Conclusions Our data show that WWTPs constitute an important source of enterococcal strains carrying antimicrobial resistance determinants, often associated with the presence of MGE, for the recipient water environment, thus increasing a pool of such genes for other organisms. The presence of HiRECCs in wastewaters and marine/river environment may indicate that adaptations gained in hospitals may be also beneficial for survival of such clones in other settings. There is an obvious need to monitor the release and spread of such strains in order to elucidate better ways to curb their dissemination. PMID:24629030

Show Me: Diversity and Isolation Indicators of Spatial Segregation within and across Missouri's School Districts

ERIC Educational Resources Information Center

Tate, William F.; Hogrebe, Mark C.

2018-01-01

Our study examines patterns of spatial segregation using diversity and isolation indicators within and across Missouri school districts. Evaluating segregation from a critical spatial perspective emphasizes the importance of place when evaluating the quality of educational opportunity for diverse student populations. The methodology involves the…

Children Reared in a Reverse Isolation Environment: Effects on Cognitive and Emotional Development.

ERIC Educational Resources Information Center

Tamaroff, Michael H.; And Others

1986-01-01

The study examined cognitive and emotional aspects of development in four infants treated from 10 to 52 months in a reverse isolation environment because of congenital severe combined immunodeficiency disease. Case material is discussed with reference to severe disruption of oral feeding experience, quality of parental involvement, and sensory…

Pathogenicity of diaporthe spp. isolates recovered from soybean (glycine max) seeds in Paraguay

USDA-ARS?s Scientific Manuscript database

Phomopsis seed decay (PSD) caused by Diaporthe longicolla (Hobbs) J.M. Santos, Vrandecic & A.J.L. Phillips has been documented as part of a soybean [Glycine max (L.) Merr.] fungal disease complex that affects the quality of soybean seed. In 2006, 16 isolates of Diaporthe were recovered from soybean...

Microscopic Analysis and Quality Assessment of Induced Sputum From Children With Pneumonia in the PERCH Study.

PubMed

Murdoch, David R; Morpeth, Susan C; Hammitt, Laura L; Driscoll, Amanda J; Watson, Nora L; Baggett, Henry C; Brooks, W Abdullah; Deloria Knoll, Maria; Feikin, Daniel R; Kotloff, Karen L; Levine, Orin S; Madhi, Shabir A; O'Brien, Katherine L; Scott, J Anthony G; Thea, Donald M; Ahmed, Dilruba; Awori, Juliet O; DeLuca, Andrea N; Ebruke, Bernard E; Higdon, Melissa M; Jorakate, Possawat; Karron, Ruth A; Kazungu, Sidi; Kwenda, Geoffrey; Hossain, Lokman; Makprasert, Sirirat; Moore, David P; Mudau, Azwifarwi; Mwaba, John; Panchalingam, Sandra; Park, Daniel E; Prosperi, Christine; Salaudeen, Rasheed; Toure, Aliou; Zeger, Scott L; Howie, Stephen R C

2017-06-15

It is standard practice for laboratories to assess the cellular quality of expectorated sputum specimens to check that they originated from the lower respiratory tract. The presence of low numbers of squamous epithelial cells (SECs) and high numbers of polymorphonuclear (PMN) cells are regarded as indicative of a lower respiratory tract specimen. However, these quality ratings have never been evaluated for induced sputum specimens from children with suspected pneumonia. We evaluated induced sputum Gram stain smears and cultures from hospitalized children aged 1-59 months enrolled in a large study of community-acquired pneumonia. We hypothesized that a specimen representative of the lower respiratory tract will contain smaller quantities of oropharyngeal flora and be more likely to have a predominance of potential pathogens compared to a specimen containing mainly saliva. The prevalence of potential pathogens cultured from induced sputum specimens and quantity of oropharyngeal flora were compared for different quantities of SECs and PMNs. Of 3772 induced sputum specimens, 2608 (69%) had <10 SECs per low-power field (LPF) and 2350 (62%) had >25 PMNs per LPF, measures traditionally associated with specimens from the lower respiratory tract in adults. Using isolation of low quantities of oropharyngeal flora and higher prevalence of potential pathogens as markers of higher quality, <10 SECs per LPF (but not >25 PMNs per LPF) was the microscopic variable most associated with high quality of induced sputum. Quantity of SECs may be a useful quality measure of induced sputum from young children with pneumonia. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

PubMed Central

Biswas, Kristi; Taylor, Michael W.; Gear, Kim

2017-01-01

The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3–V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome. PMID:28099455

Diversity of assessing circulating tumor cells (CTCs) emphasizes need for standardization: a CTC Guide to design and report trials.

PubMed

Bünger, S; Zimmermann, M; Habermann, J K

2015-09-01

Hematogenous spreading of tumor cells from primary tumors is a crucial step in the cascade to metastasis, the latter being the most limiting factor for patients' survival prognosis. Therefore, circulating tumor cells (CTCs) have become a field of intensive research. However, the process of isolation and identification of CTCs lacks standardization. This article presents an overview of 71 CTC studies reported in PUBMED since 2000 and focusing on colorectal cancer. These studies are evaluated regarding standardization of CTC isolation and identification, marker proteins used, study population and blood sample quality management, clinical performance, and quality measures. Overall, standardization of CTC assessment seems insufficient. Thus, comparability of CTC studies is hampered and results should be interpreted carefully. We here propose a standardized CTC guideline (CTC Guide) to prospectively design and report studies/trials in a harmonized form. Despite the current interstudy heterogeneity, the data indicate that CTC detection is of clinical relevance and CTCs should be considered as a surrogate prognostic marker. Many studies indicate the high potential for CTCs as prognostic markers, e.g., in colorectal cancer treatment. However, standardized, large-scale multicenter validation studies are still needed to pave the way for clinical implementation of CTC detection that could ameliorate individualized medicine regimes.