Strain-dependent airway hyperresponsiveness and a chromosome 7 locus of elevated lymphocyte numbers in cystic fibrosis transmembrane conductance regulator-deficient mice.

PubMed

Bazett, Mark; Stefanov, Anguel N; Paun, Alexandra; Paradis, Josee; Haston, Christina K

2012-03-01

We previously observed the lungs of naive BALB/cJ Cftr(tm1UNC) mice to have greater numbers of lymphocytes, by immunohistochemical staining, than did BALB wild type littermates or C57BL/6J Cftr(tm1UNC) mice. In the present study, we initially investigated whether this mutation in Cftr alters the adaptive immunity phenotype by measuring the lymphocyte populations in the lungs and spleens by FACS and by evaluating CD3-stimulated cytokine secretion, proliferation, and apoptosis responses. Next, we assessed a potential influence of this lymphocyte phenotype on lung function through airway resistance measures. Finally, we mapped the phenotype of pulmonary lymphocyte counts in BALB × C57BL/6J F2 Cftr(tm1UNC) mice and reviewed positional candidate genes. By FACS analysis, both the lungs and spleens of BALB Cftr(tm1UNC) mice had more CD3(+) (both CD4(+) and CD8(+)) cells than did littermates or C57BL/6J Cftr(tm1UNC) mice. Cftr(tm1UNC) and littermate mice of either strain did not differ in anti-CD3-stimulated apoptosis or proliferation levels. Lymphocytes from BALB Cftr(tm1UNC) mice produced more IL-4 and IL-5 and reduced levels of IFN-γ than did littermates, whereas lymphocytes from C57BL/6J Cftr(tm1UNC) mice demonstrated increased Il-17 secretion. BALB Cftr(tm1UNC) mice presented an enhanced airway hyperresponsiveness to methacholine challenge compared with littermates and C57BL/6J Cftr(tm1UNC) mice. A chromosome 7 locus was identified to be linked to lymphocyte numbers, and genetic evaluation of the interval suggests Itgal and Il4ra as candidate genes for this trait. We conclude that the pulmonary phenotype of BALB Cftr(tm1UNC) mice includes airway hyperresponsiveness and increased lymphocyte numbers, with the latter trait being influenced by a chromosome 7 locus.

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

PubMed Central

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2012-01-01

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases. PMID:21716311

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

DOE PAGES

Anantharaman, Karthik; Brown, Christopher T.; Burstein, David; ...

2016-01-28

Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugarsmore » including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we propose the provisional taxonomic assignment as ‘ Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.« less

Recombinant influenza H7 hemagglutinin containing CFLLC minidomain in the transmembrane domain showed enhanced cross-protection in mice.

PubMed

Wang, Yang; Zhang, Yun; Wu, Jialing; Lin, Ying; Wu, Zhihui; Wei, Ying; Wei, Xiaona; Qin, Jianru; Xue, Chunyi; Liu, George Dacai; Cao, Yongchang

2017-10-15

Since February 2013, H7N9 influenza virus, causing human infections with high mortality in China, has been a potential pandemic threat. The H7N9 viruses are found to diverge into distinct genotypes as other influenza viruses; thus a vaccine that can provide sufficient cross-protection against different genotypes of H7N9 viruses is urgently needed. Our previous studies demonstrated that the HA-based structural design approach by introducing a CFLLC minidomain into transmembrane domain (TM) of H1, H5 or H9 hemagglutinin (HA) proteins by replacing with H3 subtype HA TM could enhance their cross-protection. In this study, we used Sf9 insect cell expression system to express recombinant H7 HA proteins H7-53WT, in which HA gene was derived from H7N9-53 strain, and H7-53TM containing CFLLC minidomian by replacing its TM domain with H3 HA TM. We investigated whether introduction of CFLLC minidomain into H7 HA (H7-53TM) could increase its cross-reactivity and cross-protection against different genotypes of H7N9 viruses. The results showed that the H7-53TM either with or without squalene adjuvant induced increased HI antibodies, serum IgG antibodies, and IFN-γ production to a panel of 7 H7N9 viruses in mice. Vaccinated animals with H7-53TM alone showed complete protection against challenge with heterologous H7N9-MCX strain, while H7-53WT alone showed incomplete protection (80%). Furthermore, mice vaccinated with H7-53TM HA showed less body weight loss and less pulmonary lesions and inflammation after challenge with homologous or heterologous H7N9 viruses, comparing to H7-53WT. In summary, this study presents a better subunit vaccine candidate (H7-53TM) against potential H7N9 pandemic. Copyright © 2017 Elsevier B.V. All rights reserved.

The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features

PubMed Central

Kamke, Janine; Rinke, Christian; Schwientek, Patrick; Mavromatis, Kostas; Ivanova, Natalia; Sczyrba, Alexander; Woyke, Tanja; Hentschel, Ute

2014-01-01

The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake. PMID:24498082

Ammonium tetrathiomolybdate treatment targets the copper transporter ATP7A and enhances sensitivity of breast cancer to cisplatin

PubMed Central

Wong, Ada Hang-Heng; Vazquez-Ortiz, Guelaguetza; Chen, Weiping; Xu, Xiaoling; Deng, Chu-Xia

2016-01-01

Cisplatin is an effective breast cancer drug but resistance often develops over prolonged chemotherapy. Therefore, we performed a candidate approach RNAi screen in combination with cisplatin treatment to identify molecular pathways conferring survival advantages. The screen identified ATP7A as a therapeutic target. ATP7A is a copper ATPase transporter responsible for intercellular movement and sequestering of cisplatin. Pharmaceutical replacement for ATP7A by ammonium tetrathiomolybdate (TM) enhanced cisplatin treatment in breast cancer cells. Allograft and xenograft models in athymic nude mice treated with cisplatin/TM exhibited retarded tumor growth, reduced accumulation of cancer stem cells and decreased cell proliferation as compared to mono-treatment with cisplatin or TM. Cisplatin/TM treatment of cisplatin-resistant tumors reduced ATP7A protein levels, attenuated cisplatin sequestering by ATP7A, increased nuclear availability of cisplatin, and subsequently enhanced DNA damage and apoptosis. Microarray analysis of gene ontology pathways that responded uniquely to cisplatin/TM double treatment depicted changes in cell cycle regulation, specifically in the G1/S transition. These findings offer the potential to combat platinum-resistant tumors and sensitize patients to conventional breast cancer treatment by identifying and targeting the resistant tumors' unique molecular adaptations. PMID:27806319

High-spin structure, K isomers, and state mixing in the neutron-rich isotopes 173Tm and 175Tm

NASA Astrophysics Data System (ADS)

Hughes, R. O.; Lane, G. J.; Dracoulis, G. D.; Byrne, A. P.; Nieminen, P. H.; Watanabe, H.; Carpenter, M. P.; Chowdhury, P.; Janssens, R. V. F.; Kondev, F. G.; Lauritsen, T.; Seweryniak, D.; Zhu, S.

2012-11-01

High-spin states in the odd-proton thulium isotopes 173Tm and 175Tm have been studied using deep-inelastic reactions and γ-ray spectroscopy. In 173Tm, the low-lying structure has been confirmed and numerous new states have been identified, including a three-quasiparticle Kπ= 19/2- isomer with a lifetime of τ=360(100) ns at 1906 keV and a five-quasiparticle Kπ=35/2- isomer with a lifetime of τ= 175(40) ns at 4048 keV. The Kπ=35/2- state is interpreted as a t-band configuration that shows anomalously fast decays. In 175Tm, the low-lying structure has been reevaluated, a candidate state for the 9/2-[514] orbital has been identified at 1175 keV, and the 7/2-[523] bandhead has been measured to have a lifetime of τ= 460(50) ns. Newly identified high-K structures in 175Tm include a Kπ=15/2- isomer with a lifetime of τ= 64(3) ns at 947 keV and a Kπ= 23/2+ isomer with a lifetime of τ= 30(20) μs at 1518 keV. The Kπ=15/2- isomer shows relatively enhanced decays to the 7/2-[523] band that can be explained by chance mixing with the 15/2- member of the 7/2- band. Multiquasiparticle calculations have been performed for 173Tm and 175Tm, the results of which compare well with the experimentally observed high-spin states.

Animal Classification. Animal Life in Action[TM]. Schlessinger Science Library. [Videotape].

ERIC Educational Resources Information Center

2000

This 23-minute videotape for grades 5-8, presents the myriad of animal life that exists on the planet. Students can view and perform experiments and investigations that help explain animal traits and habits. They learn what the terms "kingdom", "phylum", and "order" mean, and discover how the 3.5 million-plus organisms found on Earth fit into…

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

PubMed Central

Di Rienzi, Sara C; Sharon, Itai; Wrighton, Kelly C; Koren, Omry; Hug, Laura A; Thomas, Brian C; Goodrich, Julia K; Bell, Jordana T; Spector, Timothy D; Banfield, Jillian F; Ley, Ruth E

2013-01-01

Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genome reconstruction of human fecal and subsurface aquifer metagenomic samples to obtain complete genomes for members of a new candidate phylum sibling to Cyanobacteria, for which we propose the designation ‘Melainabacteria’. Metabolic analysis suggests that the ancestors to both lineages were non-photosynthetic, anaerobic, motile, and obligately fermentative. Cyanobacterial light sensing may have been facilitated by regulators present in the ancestor of these lineages. The subsurface organism has the capacity for nitrogen fixation using a nitrogenase distinct from that in Cyanobacteria, suggesting nitrogen fixation evolved separately in the two lineages. We hypothesize that Cyanobacteria split from Melainabacteria prior or due to the acquisition of oxygenic photosynthesis. Melainabacteria remained in anoxic zones and differentiated by niche adaptation, including for symbiosis in the mammalian gut. DOI: http://dx.doi.org/10.7554/eLife.01102.001 PMID:24137540

Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester.

PubMed

Ariesyady, Herto Dwi; Ito, Tsukasa; Okabe, Satoshi

2007-04-01

Functional Bacteria and Archaea community structures of a full-scale anaerobic sludge digester were investigated by using a full-cycle 16S rRNA approach followed by microautoradiography (MAR)-fluorescent in situ hybridization (FISH) technique and micromanipulation. FISH analysis with a comprehensive set of 16S and 23S rRNA-targeted oligonucleotide probes based on 16S rRNA clone libraries revealed that the Gram-positive bacteria represented by probe HGC69A-hybridized Actinobacteria (8.5+/-1.4% of total 4', 6-diamidino-2-phenylindole (DAPI)-stained cells) and probe LGC354-hybridized Firmicutes (3.8+/-0.8%) were the major phylogenetic bacterial phyla, followed by Bacteroidetes (4.0+/-1.2%) and Chloroflexi (3.7+/-0.8%). The probe MX825-hybridized Methanosaeta (7.6+/-0.8%) was the most abundant archaeal group, followed by Methanomicrobiales (2.8+/-0.6%) and Methanobacteriaceae (2.7+/-0.4%). The functional community structures (diversity and relative abundance) of major trophic groups were quantitatively analyzed by MAR-FISH. The results revealed that glucose-degrading microbial community had higher abundance (ca. 10.6+/-4.9% of total DAPI-stained cells) and diversity (at least seven phylogenetic groups) as compared with fatty acid-utilizing microbial communities, which were more specialized to a few phylogenetic groups. Despite the dominance of Betaproteobacteria, members of Chloroflexi, Smithella, Syntrophomonas and Methanosaeta groups dominated the [(14)C]glucose-, [(14)C]propionate-, [(14)C]butyrate- and [(14)C]acetate-utilizing microorganism community, and accounted for 27.7+/-4.3%, 29.6+/-7.0%, 34.5+/-7.6% and 18.2+/-9.5%, respectively. In spite of low abundance (ca. 1%), the hitherto unknown metabolic functions of Spirochaeta and candidate phylum of TM7 as well as Synergistes were found to be glucose and acetate utilization, respectively.

2 μm emission properties and hydroxy groups quenching of Tm3+ in germanate-tellurite glass

NASA Astrophysics Data System (ADS)

Cai, Muzhi; Lu, Yu; Cao, Ruijie; Tian, Ying; Xu, Shiqing; Zhang, Junjie

2016-07-01

Tm3+ activated germanate-tellurite glasses with good thermal stability and anti-crystallization ability were prepared. Efficient 2 μm fluorescence was observed in the optimal concentration Tm3+ doped glass and the corresponding radiative properties were investigated. For Tm3+: 3F4 → 3H6 transition, high spontaneous radiative transition probability (260.75 s-1) and large emission cross section (7.66 × 10-21 cm2) were obtained from the prepared glass. According to Dexter's and Forster's theory, energy transfer microscopic parameters were computed to elucidate the observed 2 μm emissions in detail. Besides, the effect of hydroxy groups quenching was also quantificationally investigated based on simplified rate equations. Results demonstrate that the optimal concentration Tm3+ doped germanate-tellurite glass possessing excellent spectroscopic properties might be an attractive candidate for 2 μm laser or amplifier.

A Guide to the Principal Marine Fouling Organisms, with Particular Reference to Cockburn Sound, W.A.,

DTIC Science & Technology

1982-07-01

4. HYDROIDS (Phylum Cnidaria , Class Hydrozoa) 7 4.1 General 7 4.2 Common Species 7 4.3 Other Species 8 4.4 References 8 5. TUBEWORMS (Phylum Annelida...Classification of the Calcareous Sponges, British Museum (National History), London, England. 693 pp. 4. HYDROIDS (Phylum Cnidaria , Class Hydrozoa) 4.1

Development and evaluation of novel recombinant adenovirus-based vaccine candidates for infectious bronchitis virus and Mycoplasma gallisepticum in chickens.

PubMed

Zhang, Dongchao; Long, Yuqing; Li, Meng; Gong, Jianfang; Li, Xiaohui; Lin, Jing; Meng, Jiali; Gao, Keke; Zhao, Ruili; Jin, Tianming

2018-04-01

Avian infectious bronchitis caused by the infectious bronchitis virus (IBV), and mycoplasmosis caused by Mycoplasma gallisepticum (MG) are two major respiratory diseases in chickens that have resulted in severe economic losses in the poultry industry. We constructed a recombinant adenovirus that simultaneously expresses the S1 spike glycoprotein of IBV and the TM-1 protein of MG (pBH-S1-TM-1-EGFP). For comparison, we constructed two recombinant adenoviruses (pBH-S1-EGFP and pBH-TM-1-EGFP) that express either the S1 spike glycoprotein or the TM-1 protein alone. The protective efficacy of these three vaccine constructs against challenge with IBV and/or MG was evaluated in specific pathogen free chickens. Groups of seven-day-old specific pathogen free chicks were immunized twice, two weeks apart, via the oculonasal route with the pBH-S1-TM-1-EGFP, pBH-S1-EGFP, or pBH-TM-1-EGFP vaccine candidates or the commercial attenuated infectious bronchitis vaccine strain H52 and MG vaccine strain F-36 (positive controls), and challenged with virulent IBV or MG two weeks later. Interestingly, by days 7 and 14 after the booster immunization, pBH-S1-TM-1-EGFP-induced antibody titre was significantly higher (P < 0.01) compared to attenuated commercial IBV vaccine; however, there was no significant difference between the pBH-S1-TM-1-EGFP and attenuated commercial MG vaccine groups (P > 0.05). The clinical signs, the gross, and histopathological lesions scores of the adenovirus vaccine constructs were not significantly different from that of the attenuated commercial IBV or MG vaccines (positive controls) (P > 0.05). These results demonstrate the potential of the bivalent pBH-S1-TM-1-EGFP adenovirus construct as a combination vaccine against IB and mycoplasmosis.

Microbially induced iron precipitation associated with a neutrophilic spring at Borra Caves, Vishakhapatnam, India.

PubMed

Baskar, Sushmitha; Baskar, Ramanathan; Thorseth, Ingunn H; Ovreås, Lise; Pedersen, Rolf B

2012-04-01

The present investigation uncovers various pieces of evidence for the possible biologically induced mineralization in iron mats associated with a pH-neutral spring in the Borra caves, Vishakhapatnam, India. Electron microscopy [scanning electron microscopy (SEM) and transmission electron microscopy (TEM)] demonstrated large numbers of (i) hollow tubes (diameter ∼1 μm) resembling sheaths of the iron-oxidizing bacteria Leptothrix, (ii) thin (diameter <1 μm) solid fibers of uncertain origin, (iii) nanoscale subspherical to irregularly shaped particles encrusting tubes and fibers, and (iv) aggregates of broken and partially disintegrated sheaths, fibers, and particles embedded in extracellular polymeric substances (EPS) occasionally including microbial cells. X-ray microanalyses by energy dispersive spectroscopy (EDS) revealed that the mat accumulated largely Fe but also smaller amounts of Si and traces of P and Ca. Particles rich in Si and Al (possibly kaolinite) and Ca (carbonate) were also observed. High-resolution TEM/EDS of unstained ultrathin sections suggests that microbial sheaths were highly mineralized by amorphous to cryptocrystalline Fe-rich phases and less frequently by other fine-grained and fibrous authigenic claylike minerals. Total number of microorganisms in the iron mats was 5.8×10(5) cells, g sed(-1) (wet weight). Analysis of the 16S rRNA gene diversity revealed microorganisms assigned to eight different phyla [Proteobacteria (62%), Chloroflexi (8%), Bacteroidetes (7%), Planctomycetes (1%), Actinobacteria (5%), Acidobacteria (6%), Nitrospira (1%), Firmicutes (5%)]. Within the Proteobacteria, Betaproteobacteria was the predominant class, which accounted for 28% of the sequences. Within this class some obvious similarities between the obtained sequences and sequences from other cave systems could be seen, especially sequences affiliated with Leptothrix, Siderooxidans, Crenothrix, Comamonadaceae, Dechloromonas, and many uncultured Betaproteobacteria. Four (4%) of the sequences could not be assigned to phylum level but were affiliating with the candidate division TM7 (2%), candidate division OP11 (1%), and candidate division WWE3 (1%). The results allow us to infer a possible relationship of microbial sheaths, EPS, and the iron precipitates to microbial community diversity in the Borra cave springs. Understanding biogenic iron oxides in caves has important astrobiological applications as it provides a potential tool for the detection of extraterrestrial life.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Benthic and Sedimentologic Studies on the Charleston Harbor Ocean Disposal Area, Charleston Harbor Deepening Project.

DTIC Science & Technology

1979-08-01

Nolella stipate 1 Phylum S ipuncula Sipunculid (undet.) 14 Phylum Echiura Echiurid (undet.) 1 Phylum-. Annelida Hvdroides dianthus 27 Sabellaria...undet.) LEr-idomotus subievi.s Sab)ellaria \\’ulgaris HIvdroides dianthus 9 lu- Mloliusca * Polinices duplicatus0 Modiclus mocilolus squarnosus...tenuis Microporella ciliata Schizoporella cornuta Phvlum Annelida H-vdroides dianthus Sabelliaria x’ulgaris 41Ph’iu MToi 7lusca Creoidula olana Phylum

Bacteria and archaea paleomicrobiology of the dental calculus: a review.

PubMed

Huynh, H T T; Verneau, J; Levasseur, A; Drancourt, M; Aboudharam, G

2016-06-01

Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Population variation revealed high-altitude adaptation of Tibetan mastiffs.

PubMed

Li, Yan; Wu, Dong-Dong; Boyko, Adam R; Wang, Guo-Dong; Wu, Shi-Fang; Irwin, David M; Zhang, Ya-Ping

2014-05-01

With the assistance of their human companions, dogs have dispersed into new environments during the expansion of human civilization. Tibetan Mastiff (TM), a native of the Tibetan Plateau, was derived from the domesticated Chinese native dog and, like Tibetans, has adapted to the extreme environment of high altitude. Here, we genotyped genome-wide single-nucleotide polymorphisms (SNPs) from 32 TMs and compared them with SNPs from 20 Chinese native dogs and 14 gray wolves (Canis lupus). We identified 16 genes with signals of positive selection in the TM, with 12 of these candidate genes associated with functions that have roles in adaptation to high-altitude adaptation, such as EPAS1, SIRT7, PLXNA4, and MAFG that have roles in responses to hypoxia. This study provides important information on the genetic diversity of the TM and potential mechanisms for adaptation to hypoxia.

Thematic mapper studies band correlation analysis

NASA Technical Reports Server (NTRS)

Ungar, S. G.; Kiang, R.

1976-01-01

Spectral data representative of thematic mapper candidate bands 1 and 3 to 7 were obtained by selecting appropriate combinations of bands from the JSC 24 channel multispectral scanner. Of all the bands assigned, only candidate bands 4 (.74 mu to .80 mu) and 5 (.80 mu to .91 mu) showed consistently high intercorrelation from region to region and time to time. This extremely high correlation persisted when looking at the composite data set in a multitemporal, multilocation domain. The GISS investigations lend positive confirmation to the hypothesis, that TM bands 4 and 5 are redundant.

Physiology and phylogeny of the candidate phylum "Atribacteria" (formerly OP9/JS1) inferred from single-cell genomics and metagenomics

NASA Astrophysics Data System (ADS)

Dodsworth, J. A.; Murugapiran, S.; Blainey, P. C.; Nobu, M.; Rinke, C.; Schwientek, P.; Gies, E.; Webster, G.; Kille, P.; Weightman, A.; Liu, W. T.; Hallam, S.; Tsiamis, G.; Swingley, W.; Ross, C.; Tringe, S. G.; Chain, P. S.; Scholz, M. B.; Lo, C. C.; Raymond, J.; Quake, S. R.; Woyke, T.; Hedlund, B. P.

2014-12-01

Single-cell sequencing and metagenomics have extended the genomics revolution to yet-uncultivated microorganisms and provided insights into the coding potential of this so-called "microbial dark matter", including microbes belonging candidate phyla with no cultivated representatives. As more datasets emerge, comparison of individual genomes from different lineages and habitats can provide insight into the phylogeny, conserved features, and potential metabolic diversity of candidate phyla. The candidate bacterial phylum OP9 was originally found in Obsidian Pool, Yellowstone National Park, and it has since been detected in geothermal springs, petroleum reservoirs, and engineered thermal environments worldwide. JS1, another uncultivated bacterial lineage affiliated with OP9, is often abundant in marine sediments associated with methane hydrates, hydrocarbon seeps, and on continental margins and shelves, and is found in other non-thermal marine and subsurface environments. The phylogenetic relationship between OP9, JS1, and other Bacteria has not been fully resolved, and to date no axenic cultures from these lineages have been reported. Recently, 31 single amplified genomes (SAGs) from six distinct OP9 and JS1 lineages have been obtained using flow cytometric and microfluidic techniques. These SAGs were used to inform metagenome binning techniques that identified OP9/JS1 sequences in several metagenomes, extending genomic coverage in three of the OP9 and JS1 lineages. Phylogenomic analyses of these SAG and metagenome bin datasets suggest that OP9 and JS1 constitute a single, deeply branching phylum, for which the name "Atribacteria" has recently been proposed. Overall, members of the "Atribacteria" are predicted to be heterotrophic anaerobes without the capacity for respiration, with some lineages potentially specializing in secondary fermentation of organic acids. A set of signature "Atribacteria" genes was tentatively identified, including components of a bacterial microcompartments gene cluster that may be involved in carbohydrate catabolism. The "Atribacteria" may play important roles in biomass processing in anaerobic geothermal and subsurface environments.

A One-Piece Lunar Regolith Bag Garage Prototype

NASA Technical Reports Server (NTRS)

Smithers, G. A.; Nehls, M. K.; Hovater, M. A.; Evans, S. W.; Miller, J. S.; Broughton, R. M., Jr.; Beale, D.; Kilinc-Balci, F.

2007-01-01

Shelter structures on the moon, even in early phases of exploration, should incorporate lunar materials as much as possible. This Technical Memorandum details the design and construction of a prototype for a one-piece regolith bag unpressurized garage concept and a materials testing program to investigate six candidate fabrics to learn how they might perform in the lunar environment. The conceptualization was that a lightweight fabric form be launched from Earth and landed on the lunar surface to be robotically filled with raw lunar regolith. Regolith bag fabric candidates included: Vectran(TM), Nextel(TM), Gore PTFE Fabric(TM), Zylon(TM), Twaron(TM), and Nomex(TM). Tensile (including post radiation exposure), fold, abrasion, and hypervelocity impact testing were performed under ambient conditions, and also performed under cold and elevated temperatures. In some cases, Johnson Space Center lunar simulant (JSC-1) was used in conjunction with testing. A series of preliminary structures was constructed during final prototype design based on the principles of the classic masonry arch. The prototype was constructed of Kevlar(TM) and filled with vermiculite. The structure is free-standing, but has not yet been load tested. Future plans would be to construct higher fidelity prototypes and to conduct appropriate tests of the structure.

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

PubMed

Wang, Zhiping; Guo, Feng; Liu, Lili; Zhang, Tong

2014-01-01

Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB) cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

Bacterial Community Associated with the Intestinal Tract of Chinese Mitten Crab (Eriocheir sinensis) Farmed in Lake Tai, China

PubMed Central

Chen, Xiaobing; Di, Panpan; Wang, Hongming; Li, Bailin; Pan, Yingjie; Yan, Shuling; Wang, Yongjie

2015-01-01

Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal ＞95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host. PMID:25875449

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

PubMed Central

Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M.; Woyke, Tanja; Kyrpides, Nikos C.; Ivanova, Natalia N.

2016-01-01

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. PMID:26814032

The First Complete Genome Sequence of the Class Fimbriimonadia in the Phylum Armatimonadetes

PubMed Central

Im, Wan-Taek; Wang, Sheng-Yue; Zhao, Guo-Ping; Zheng, Hua-Jun; Quan, Zhe-Xue

2014-01-01

In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes, formerly called as candidate phylum OP10. The complete genome contains a single circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew inversion which was usually observed in archaea was found. The predicted gene functions suggest that the organism lacks the ability to synthesize histidine, and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal proteins indicated that strain Gsoil 348T represents a deeply branching lineage of sufficient divergence with other phyla, but also strongly involved in superphylum Terrabacteria. PMID:24967843

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs.

PubMed

Eloe-Fadrosh, Emiley A; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F; Hedlund, Brian P; Dekas, Anne E; Grasby, Stephen E; Brady, Allyson L; Dong, Hailiang; Briggs, Brandon R; Li, Wen-Jun; Goudeau, Danielle; Malmstrom, Rex; Pati, Amrita; Pett-Ridge, Jennifer; Rubin, Edward M; Woyke, Tanja; Kyrpides, Nikos C; Ivanova, Natalia N

2016-01-27

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

DOE PAGES

Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; ...

2016-01-27

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (' Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestylemore » with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

Candidate OP Phyla: Importance, Ecology and Cultivation Prospects.

PubMed

Rohini Kumar, M; Saravanan, V S

2010-10-01

OP phyla were created in the domain bacteria, based on the group of 16S rRNA gene sequences recovered from the Obsidian Pool. However, due to the lack of cultured representative it is referred to as candidate phyla. Wider ecological occurrence was predicted for the OP phyla, especially OP3, OP10 and OP11. Recently, members of phylum OP5 and OP10 were cultured, providing clues to their cultivation prospects. At last the bioprospecting potentials of the OP members are discussed herein.

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

PubMed

Ji, Boyang; Zhang, Sheng-Da; Zhang, Wei-Jia; Rouy, Zoe; Alberto, François; Santini, Claire-Lise; Mangenot, Sophie; Gagnot, Séverine; Philippe, Nadège; Pradel, Nathalie; Zhang, Lichen; Tempel, Sébastien; Li, Ying; Médigue, Claudine; Henrissat, Bernard; Coutinho, Pedro M; Barbe, Valérie; Talla, Emmanuel; Wu, Long-Fei

2017-03-01

Magnetotactic bacteria (MTB) are a group of phylogenetically and physiologically diverse Gram-negative bacteria that synthesize intracellular magnetic crystals named magnetosomes. MTB are affiliated with three classes of Proteobacteria phylum, Nitrospirae phylum, Omnitrophica phylum and probably with the candidate phylum Latescibacteria. The evolutionary origin and physiological diversity of MTB compared with other bacterial taxonomic groups remain to be illustrated. Here, we analysed the genome of the marine magneto-ovoid strain MO-1 and found that it is closely related to Magnetococcus marinus MC-1. Detailed analyses of the ribosomal proteins and whole proteomes of 390 genomes reveal that, among the Proteobacteria analysed, only MO-1 and MC-1 have coding sequences (CDSs) with a similarly high proportion of origins from Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Gammaproteobacteria. Interestingly, a comparative metabolic network analysis with anoxic network enzymes from sequenced MTB and non-MTB successfully allows the eventual prediction of an organism with a metabolic profile compatible for magnetosome production. Altogether, our genomic analysis reveals multiple origins of MO-1 and M. marinus MC-1 genomes and suggests a metabolism-restriction model for explaining whether a bacterium could become an MTB upon acquisition of magnetosome encoding genes. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking

PubMed Central

Ohashi, Akiko; Parks, Donovan H.; Yamauchi, Toshihiro; Tyson, Gene W.

2015-01-01

Filamentous cells belonging to the candidate bacterial phylum KSB3 were previously identified as the causative agent of fatal filament overgrowth (bulking) in a high-rate industrial anaerobic wastewater treatment bioreactor. Here, we obtained near complete genomes from two KSB3 populations in the bioreactor, including the dominant bulking filament, using differential coverage binning of metagenomic data. Fluorescence in situ hybridization with 16S rRNA-targeted probes specific for the two populations confirmed that both are filamentous organisms. Genome-based metabolic reconstruction and microscopic observation of the KSB3 filaments in the presence of sugar gradients indicate that both filament types are Gram-negative, strictly anaerobic fermenters capable of non-flagellar based gliding motility, and have a strikingly large number of sensory and response regulator genes. We propose that the KSB3 filaments are highly sensitive to their surroundings and that cellular processes, including those causing bulking, are controlled by external stimuli. The obtained genomes lay the foundation for a more detailed understanding of environmental cues used by KSB3 filaments, which may lead to more robust treatment options to prevent bulking. PMID:25650158

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

NASA Astrophysics Data System (ADS)

Jahn, Martin T.; Markert, Sebastian M.; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas

2016-10-01

Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.

Intracellular distribution of TM4SF1 and internalization of TM4SF1-antibody complex in vascular endothelial cells

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

Sciuto, Tracey E.; Merley, Anne; Lin, Chi-Iou

2015-09-25

Transmembrane-4 L-six family member-1 (TM4SF1) is a small plasma membrane-associated glycoprotein that is highly and selectively expressed on the plasma membranes of tumor cells, cultured endothelial cells, and, in vivo, on tumor-associated endothelium. Immunofluorescence microscopy also demonstrated TM4SF1 in cytoplasm and, tentatively, within nuclei. With monoclonal antibody 8G4, and the finer resolution afforded by immuno-nanogold transmission electron microscopy, we now demonstrate TM4SF1 in uncoated cytoplasmic vesicles, nuclear pores and nucleoplasm. Because of its prominent surface location on tumor cells and tumor-associated endothelium, TM4SF1 has potential as a dual therapeutic target using an antibody drug conjugate (ADC) approach. For ADC to bemore » successful, antibodies reacting with cell surface antigens must be internalized for delivery of associated toxins to intracellular targets. We now report that 8G4 is efficiently taken up into cultured endothelial cells by uncoated vesicles in a dynamin-dependent, clathrin-independent manner. It is then transported along microtubules through the cytoplasm and passes through nuclear pores into the nucleus. These findings validate TM4SF1 as an attractive candidate for cancer therapy with antibody-bound toxins that have the capacity to react with either cytoplasmic or nuclear targets in tumor cells or tumor-associated vascular endothelium. - Highlights: • Anti-TM4SF1 antibody 8G4 was efficiently taken up by cultured endothelial cells. • TM4SF1–8G4 internalization is dynamin-dependent but clathrin-independent. • TM4SF1–8G4 complexes internalize along microtubules to reach the perinuclear region. • Internalized TM4SF1–8G4 complexes pass through nuclear pores into the nucleus. • TM4SF1 is an attractive candidate for ADC cancer therapy.« less

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

Wrighton, Kelly C.; Castelle, Cindy; Wilkins, Michael J.

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge, and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, Colorado, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via two acetate-based biostimulation treatments. Samples weremore » collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include genomes from a new phylum (ACD20), phylogenetically novel members of the Chloroflexi and Bacteroidetes, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER, and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate, and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen currency in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate, and iron reduction. Thus, fermentation carried out by previously unstudied members of sediment microbial communities may be an important driver of diverse subsurface biogeochemical cycles.« less

Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

PubMed

Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

2017-01-01

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.

NIR to NIR upconversion in KYb2F7: RE3+ (RE = Tm, Er) nanoparticles for biological imaging

NASA Astrophysics Data System (ADS)

Pedraza, F.; Yust, B.; Tsin, A.; Sardar, D.

2014-03-01

Until recently, many contrast agents widely used in biological imaging have absorbed and emitted in the visible region, limiting their usefulness for deeper tissue imaging. In order to push the boundaries of deep tissue imaging with non-ionizing radiation, contrast agents in the near infrared (NIR) regime, which is not strongly absorbed or scattered by most tissues, are being sought after. Upconverting nanoparticles (UCNPs) are attractive candidates since their upconversion emission is tunable with a very narrow bandwidth and they do not photobleach or blink. The upconversion produced by the nanoparticles can be tailored for NIR to NIR by carefully choosing the lanthanide dopants and dopant ratios such as KYb2F7: RE3+ (RE = Tm, Er). Spectroscopic characterization was done by analyzing absorption, fluorescence, and quantum yield data. In order to study the toxicity of the nanoparticles Monkey Retinal Endothelial Cells (MREC) were cultivated in 24 well plates and then treated with nanoparticles at different concentrations in triplicate to obtain the optimal concentration for in vivo experiments. It will be shown that these UCNPs do not elicit a strong toxic response such as quantum dots and some noble metal nanoparticles. 3-D optical slices of nanoparticle treated fibroblast cells were imaged using a confocal microscope where the nucleus and cytoplasm were stained with DAPI and Alexa Fluor respectively. These results presented support the initial assumption, which suggests that KYb2F7: RE3+ would be excellent candidates for NIR contrast agents.

Lack of P4H-TM in mice results in age-related retinal and renal alterations.

PubMed

Leinonen, Henri; Rossi, Maarit; Salo, Antti M; Tiainen, Päivi; Hyvärinen, Jaana; Pitkänen, Marja; Sormunen, Raija; Miinalainen, Ilkka; Zhang, Chi; Soininen, Raija; Kivirikko, Kari I; Koskelainen, Ari; Tanila, Heikki; Myllyharju, Johanna; Koivunen, Peppi

2016-09-01

Age-related macular degeneration (AMD), affecting the retinal pigment epithelium (RPE), is the leading cause of blindness in middle-aged and older people in developed countries. Genetic and environmental risk factors have been identified, but no effective cure exists. Using a mouse model we show that a transmembrane prolyl 4-hydroxylase (P4H-TM), which participates in the oxygen-dependent regulation of the hypoxia-inducible factor (HIF), is a potential novel candidate gene for AMD. We show that P4h-tm had its highest expression levels in the mouse RPE and brain, heart, lung, skeletal muscle and kidney. P4h-tm -/- mice were fertile and had a normal life span. Lack of P4h-tm stabilized HIF-1α in cortical neurons under normoxia, while in hypoxia it increased the expression of certain HIF target genes in tissues with high endogenous P4h-tm expression levels more than in wild-type mice. Renal erythropoietin levels increased in P4h-tm -/- mice with aging, but the resulting ∼2-fold increase in erythropoietin serum levels did not lead to erythrocytosis. Instead, accumulation of lipid-containing lamellar bodies in renal tubuli was detected in P4h-tm -/- mice with aging, resulting in inflammation and fibrosis, and later glomerular sclerosis and albuminuria. Lack of P4h-tm was associated with retinal thinning, rosette-like infoldings and drusen-like structure accumulation in RPE with aging, as is characteristic of AMD. Photoreceptor recycling was compromised, and electroretinograms revealed functional impairment of the cone pathway in adult P4h-tm -/- mice and cone and rod deficiency in middle-aged mice. P4H-TM is therefore imperative for normal vision, and potentially a novel candidate for age-induced diseases, such as AMD. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A One-Piece Lunar Regolith-Bag Garage Prototype

NASA Technical Reports Server (NTRS)

Smithers, Gweneth A.; Nehls, Mary K.; Hovater, Mary A.; Evans, Steven W.; Miller, J. Scott; Broughton, Roy M., Jr.; Beale, David; Killinc-Balci, Fatma

2006-01-01

Shelter structures on the moon, even in early phases of exploration, should incorporate lunar materials as much as possible. We designed and constructed a prototype for a one-piece regolith-bag unpressurized garage concept, and, in parallel, we conducted a materials testing program to investigate six candidate fabrics to learn how they might perform in the lunar environment. In our concept, a lightweight fabric form is launched from Earth to be landed on the lunar surface and robotically filled with raw lunar regolith. In the materials testing program, regolith-bag fabric candidates included: VectranTM, NextelTM, Gore PTFE FabricTM, ZylonTM TwaronTM and NomexTM. Tensile (including post radiation exposure), fold, abrasion, and hypervelocity impact testing were performed under ambient conditions, and, within our current means, we also performed these tests under cold and elevated temperatures. In some cases, lunar simulant (JSC-1) was used in conjunction with testing. Our ambition is to continuously refine our testing to reach lunar environmental conditions to the extent possible. A series of preliminary structures were constructed during design of the final prototype. Design is based on the principles of the classic masonry arch. The prototype was constructed of KevlarTM and filled with vermiculite (fairly close to the weight of lunar regolith on the moon). The structure is free-standing, but has not yet been load tested. Our plan for the future would be to construct higher fidelty mockups with each iteration, and to conduct appropriate tests of the structure.

A One-Piece Lunar Regolith-Bag Garage Prototype

NASA Technical Reports Server (NTRS)

Smithers, Gweneth A.; Nehls, Mary K.; Hovater, Mary A.; Evans, Steven W.; Miller, J. Scott; Broughton, Roy M.; Beale, David; Killing-Balci, Fatma

2007-01-01

Shelter structures on the moon, even in early phases of exploration, should incorporate lunar materials as much as possible. We designed and constructed a prototype for a one-piece regolith-bag unpressurized garage concept, and, in parallel, we conducted a materials testing program to investigate six candidate fabrics to learn how they might perform in the lunar environment. In our concept, a lightweight fabric form is launched from Earth to be landed on the lunar surface and robotically filled with raw lunar regolith. In the materials testing program, regolith-bag fabric candidates included: Vectran(TM), Nextel(TM), Gore PTFE Fabric(TM), Zylon(TM), Twaron(TM), and Nomex(TM). Tensile (including post radiation exposure), fold, abrasion, and hypervelocity impact testing were performed under ambient conditions, and, within our current means, we also performed these tests under cold and elevated temperatures. In some cases, lunar simulant (JSC-1) was used in conjunction with testing. Our ambition is to continuously refine our testing to reach lunar environmental conditions to the extent possible. A series of preliminary structures were constructed during design of the final prototype. Design is based on the principles of the classic masonry arch. The prototype was constructed of Kevlar(TM) and filled with vermiculite (fairly close to the weight of lunar regolith on the moon). The structure is free-standing, but has not yet been load tested. Our plan for the future would be to construct higher fidelity mockups with each iteration, and to conduct appropriate tests of the structure.

Energy transfer and colour tunability in UV light induced Tm3 +/Tb3 +/Eu3 +: ZnB glasses generating white light emission

NASA Astrophysics Data System (ADS)

Naresh, V.; Gupta, Kiran; Parthasaradhi Reddy, C.; Ham, Byoung S.

2017-03-01

A promising energy transfer (Tm3 + → Tb3 + → Eu3 +) approach is brought forward to generate white light emission under ultraviolet (UV) light excitation for solid state lightening. Tm3 +/Tb3 +/Eu3 + ions are combinedly doped in zinc borate glass system in view of understanding energy transfer process resulting in white light emission. Zinc borate (host) glass displayed optical and luminescence properties due to formation of Zn(II)x-[O(- II)]y centres in the ZnB glass matrix. At 360 nm (UV) excitation, triply doped Tm3 +/Tb3 +/Eu3 +: ZnB glasses simultaneously shown their characteristic emission bands in blue (454 nm: 1D2 → 3F4), green (547 nm: 5D4 → 7F5) and red (616 nm: 5D0 → 7F2) regions. In triple ions doped glasses, energy transfer dynamics is discussed in terms of Forster-Dexter theory, excitation & emission profiles, lifetime curves and from partial energy level diagram of three ions. The role of Tb3 + in ET from Tm3 + → Eu3 + was discussed using branch model. From emission decay analysis, energy transfer probability (P) and efficiency (η) were evaluated. Colour tunability from blue to white on varying (Tb3 +, Eu3 +) content is demonstrated from Commission Internationale de L'Eclairage (CIE) chromaticity coordinates. Based on chromaticity coordinates, other colour related parameters like correlated colour temperature (CCT) and colour purity are also computed for the studied glass samples. An appropriate blending of such combination of rare earth ions could show better suitability as potential candidates in achieving multi-colour and warm/cold white light emission for white LEDs application in the field of solid state lightening.

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum

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

Rodionova, Irina A.; Li, Xiaoqing; Plymale, Andrew E.

Bacteria from the Chloroflexi phylum are dominant members of phototrophic microbial mat communities in terrestrial thermal environments. Vitamins of B-group are key intermediates (precursors) in the biosynthesis of indispensable enzyme cofactors driving numerous metabolic processes in all forms of life. A genomics-based reconstruction and comparative analysis of respective biosynthetic and salvage pathways and riboswitch regulons in over 20 representative Chloroflexi genomes revealed a widespread auxotrophy for some of the vitamins. The most prominent predicted phenotypic signature, auxotrophy for vitamins B1 and B7 was experimentally confirmed for the best studied model organism Chloroflexus aurantiacus. These observations along with identified candidate genesmore » for the respective uptake transporters pointed to B vitamin exchange as an important aspect of syntrophic metabolism in microbial communities. Inferred specificities of homologous substrate-binding components of ABC transporters for vitamins B1 (ThiY) and B2 (RibY) were verified by thermofluorescent shift approach. A functional activity of the thiamine-specific transporter ThiXYZ from C. aurantiacus was experimentally verified by genetic complementation in E. coli. Expanding the integrative approach, which was applied here for a comprehensive analysis of B-vitamin metabolism in Chloroflexi would allow reconstruction of metabolic interdependencies in microbial communities.« less

2.5 MHz Line-Width High-energy, 2 Micrometer Coherent Wind Lidar Transmitter

NASA Technical Reports Server (NTRS)

Petros, Mulugeta; Yu, Jirong; Trieu, Bo; Bai, Yingxin; Petzar, Paul; Singh, Upendra N.; Reithmaier, Karl

2007-01-01

2 micron solid-state lasers are the primary choice for coherent Doppler wind detection. As wind lidars, they are used for wake vortex and clear air turbulence detection providing air transport safety. In addition, 2 micron lasers are one of the candidates for CO2 detection lidars. The rich CO2 absorption line around 2 micron, combined with the long upper state life of time, has made Ho based 2 micron lasers a viable candidate for CO2 sensing DIAL instrument. The design and fabrication of a compact coherent laser radar transmitter for Troposphere wind sensing is under way. This system is hardened for ground as well as airborne applications. As a transmitter for a coherent wind lidar, this laser has stringent spectral line width and beam quality requirements. Although the absolute wavelength does not have to be fixed for wind detection, to maximize return signal, the output wavelength should avoid atmospheric CO2 and H2O absorption lines. The base line laser material is Ho:Tm:LuLF which is an isomorph of Ho:Tm:YLF. LuLF produces 20% more output power than Ho:Tm:YLF. In these materials the Tm absorption cross-section, the Ho emission cross-section, the Tm to Ho energy transfer parameters and the Ho (sup 5) I (sub 7) radiative life time are all identical. However, the improved performance of the LuLF is attributed to the lower thermal population in the (sup 5) I (sub 8) manifold. It also provides higher normal mode to Q-switch conversion than YLF at high pump energy indicating a lower up-conversion. The laser architecture is composed of a seed laser, a ring oscillator, and a double pass amplifier. The seed laser is a single longitudinal mode with a line width of 13 KHz. The 100mJ class oscillator is stretched to 3 meters to accommodate the line-width requirement without compromising the range resolution of the instrument. The amplifier is double passed to produce greater than 300mJ energy.

Molecular cloing and bioinformatics analysis of lactate dehydrogenase from Taenia multiceps.

PubMed

Guo, Cheng; Wang, Yu; Huang, Xing; Wang, Ning; Yan, Ming; He, Ran; Gu, Xiaobin; Xie, Yue; Lai, Weimin; Jing, Bo; Peng, Xuerong; Yang, Guangyou

2017-10-01

Coenurus cerebralis, the larval stage (metacestode or coenurus) of Taenia multiceps, parasitizes sheep, goats, and other ruminants and causes coenurosis. In this study, we isolated and characterized complementary DNAs that encode lactate dehydrogenase A (Tm-LDHA) and B (Tm-LDHB) from the transcriptome of T. multiceps and expressed recombinant Tm-LDHB (rTm-LDHB) in Escherichia coli. Bioinformatic analysis showed that both Tm-LDH genes (LDHA and LDHB) contain a 996-bp open reading frame and encode a protein of 331 amino acids. After determination of the immunogenicity of the recombinant Tm-LDHB, an indirect enzyme-linked immunosorbent assay (ELISA) was developed for preliminary evaluation of the serodiagnostic potential of rTm-LDHB in goats. However, the rTm-LDHB-based indirect ELISA developed here exhibited specificity of only 71.42% (10/14) and sensitivity of 1:3200 in detection of goats infected with T. multiceps in the field. This study is the first to describe LDHA and LDHB of T. multiceps; meanwhile, our results indicate that rTm-LDHB is not a specific antigen candidate for immunodiagnosis of T. multiceps infection in goats.

Molecular analyses of the microbial community composition of an anoxic basin of a municipal wastewater treatment plant reveal a novel lineage of proteobacteria.

PubMed

Chouari, Rakia; Le Paslier, Denis; Daegelen, Patrick; Dauga, Catherine; Weissenbach, Jean; Sghir, Abdelghani

2010-08-01

A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within the anoxic basin.

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

Lin, Qingqing; Li, Huilin; Wang, Tong

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

PubMed

Serkebaeva, Yulia M; Kim, Yongkyu; Liesack, Werner; Dedysh, Svetlana N

2013-01-01

Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (pH 4.0) Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs) determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively), Alphaproteobacteria (15.9±1.7% and 25.8±1.4%), Actinobacteria (9.5±2.0% and 10.7±0.5%), Verrucomicrobia (8.5±1.4% and 0.6±0.2%), Planctomycetes (5.8±0.4% and 9.7±0.6%), Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%), and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%). The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs) than in the anoxic subsurface peat (483 OTUs), with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and subsurface layers of northern peatlands are highly diverse and taxonomically distinct, reflecting the different abiotic conditions in microhabitats within the peat profile.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

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

Hu, Ping; Tom, Lauren; Singh, Andrea

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to bemore » the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of theAcetothermia(OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylumParcubacteria(OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, includingMicrogenomates(OP11),Atribacteria(OP9), candidate phyla TA06 and WS6, andMarinimicrobia(SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. In conclusion, we show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.« less

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.

PubMed

Hu, Ping; Tom, Lauren; Singh, Andrea; Thomas, Brian C; Baker, Brett J; Piceno, Yvette M; Andersen, Gary L; Banfield, Jillian F

2016-01-19

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to be the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of the Acetothermia (OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylum Parcubacteria (OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, including Microgenomates (OP11), Atribacteria (OP9), candidate phyla TA06 and WS6, and Marinimicrobia (SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. We show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes. Copyright © 2016 Hu et al.

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs

DOE PAGES

Hu, Ping; Tom, Lauren; Singh, Andrea; ...

2016-01-19

Oil reservoirs are major sites of methane production and carbon turnover, processes with significant impacts on energy resources and global biogeochemical cycles. We applied a cultivation-independent genomic approach to define microbial community membership and predict roles for specific organisms in biogeochemical transformations in Alaska North Slope oil fields. Produced water samples were collected from six locations between 1,128 m (24 to 27°C) and 2,743 m (80 to 83°C) below the surface. Microbial community complexity decreased with increasing temperature, and the potential to degrade hydrocarbon compounds was most prevalent in the lower-temperature reservoirs. Sulfate availability, rather than sulfate reduction potential, seems to bemore » the limiting factor for sulfide production in some of the reservoirs under investigation. Most microorganisms in the intermediate- and higher-temperature samples were related to previously studied methanogenic and nonmethanogenic archaea and thermophilic bacteria, but one candidate phylum bacterium, a member of theAcetothermia(OP1), was present in Kuparuk sample K3. The greatest numbers of candidate phyla were recovered from the mesothermic reservoir samples SB1 and SB2. We reconstructed a nearly complete genome for an organism from the candidate phylumParcubacteria(OD1) that was abundant in sample SB1. Consistent with prior findings for members of this lineage, the OD1 genome is small, and metabolic predictions support an obligately anaerobic, fermentation-based lifestyle. At moderate abundance in samples SB1 and SB2 were members of bacteria from other candidate phyla, includingMicrogenomates(OP11),Atribacteria(OP9), candidate phyla TA06 and WS6, andMarinimicrobia(SAR406). The results presented here elucidate potential roles of organisms in oil reservoir biological processes. The activities of microorganisms in oil reservoirs impact petroleum resource quality and the global carbon cycle. In conclusion, we show that bacteria belonging to candidate phyla are present in some oil reservoirs and provide the first insights into their potential roles in biogeochemical processes based on several nearly complete genomes.« less

Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum.

PubMed

Chen, Shisheng; Guo, Yan; Briggs, Jordan; Dubach, Felix; Chao, Shiaoman; Zhang, Wenjun; Rouse, Matthew N; Dubcovsky, Jorge

2018-03-01

The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5A m S, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7A m L, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5A m S that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC-NBS-LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60.

Characterisation of the human oral microbiome in patients with coronary artery disease using next-generation sequencing of 16SrRNA amplicons.

PubMed

Menon, Thangam; Gopalakrishnan, Sathya Narayanan; Balasubramanian, Rayvathy; Justin, Stalin Roy

2017-01-01

Oral health is suspected to be linked to heart disease since species of bacteria that cause periodontitis and dental caries have been found in the atherosclerotic plaque in arteries in the heart. The aim of this study was to characterize the oral microbiome in patients with coronary artery disease (CAD) and in a patient with dental caries (DC) without any clinical symptoms of CAD. DNA was extracted from the oral swabs collected from the patients and sequencing was performed by next generation sequencing method using Illumina (MiSeq) platform. The resulting sequencing data set was analysed using QIIME. A total of 31 phyla were found in all the samples. The predominant phylum found in both CAD and DC was Firmicutes (46.09% & 38.98%), Proteobacteria (17.73% & 9.79%), Fusobacteria (13.44% & 17.95%), Bacteroidetes (11.82% & 22.73%), Actinobacteria (8.33% & 7.71%) and TM7 (2.25% & 2.71%). We found a similarity in the bacterial diversity in the two groups of patients. A comparison of the oral microbiome in patients with CAD and DC shows a similarity in the composition of the oral microbiota with variations in the proportion of a few genera.

Isolation and phylogenetic characterization of iron-sulfur-oxidizing heterotrophic bacteria indigenous to nickel laterite ores of Sulawesi, Indonesia: Implications for biohydrometallurgy

NASA Astrophysics Data System (ADS)

Chaerun, Siti Khodijah; Hung, Sutina; Mubarok, Mohammad Zaki; Sanwani, Edy

2015-09-01

The main objective of this study was to isolate and phylogenetically identify the indigenous iron-sulfur-oxidizing heterotrophic bacteria capable of bioleaching nickel from laterite mineral ores. The bacteria were isolated from a nickel laterite mine area in South Sulawesi Province, Indonesia. Seven bacterial strains were successfully isolated from laterite mineral ores (strains SKC/S-1 to SKC/S-7) and they were capable of bioleaching of nickel from saprolite and limonite ores. Using EzTaxon-e database, the 16S rRNA gene sequences of the seven bacterial strains were subjected to phylogenetic analysis, resulting in a complete hierarchical classification system, and they were identified as Pseudomonas taiwanensis BCRC 17751 (98.59% similarity), Bacillus subtilis subsp. inaquosorum BGSC 3A28 (99.14% and 99.32% similarities), Paenibacillus pasadenensis SAFN-007 (98.95% and 99.33% similarities), Bacillus methylotrophicus CBMB 205 (99.37% similarity), and Bacillus altitudinis 41KF2b (99.37% similarity). It is noteworthy that members of the phylum Firmicutes (in particular the genus Bacillus) predominated in this study, therefore making them to have the high potential to be candidates for the bioleaching of nickel from laterite mineral ores. To our knowledge, this is the first report on the predominance of the phylum Firmicutes in the Sulawesi laterite mineral ores.

Preliminary evaluation of the landsat-4 thematic mapper data for mineral exploration

USGS Publications Warehouse

Podwysocki, M.H.; Power, M.S.; Jones, O.D.

1985-01-01

Landsat-4 Thematic Mapper (TM) data recorded over an arid terrain were analyzed to determine the applicability of using of TM data for identifying and mapping hydrothermally altered, potentially mineralized rocks. Clays, micas, and other minerals bearing the OH anion in specific crystal lattice positions have absorption bands in the 2.2-??m region (TM channel 7, TM7) and commonly lack features in the 1.6-??m region (TM5). Channel ratios TM5/TM7, TM5/TM4, and TM3/TM1 were combined into a color-ratio-composite (CRC) image and used to distinguish hydrothermally altered rocks, unaltered rocks, and vegetation. These distinctions are made possible by using the TM5 and TM7, channels which are not available in the Landsat multispectral scanner (MSS). Digital masking was used to eliminate ambiguities due to water and shadows. However, some ambiguities in identification resulted between altered volcanic rocks and unaltered sedimentary deposits that contained clays, carbonates, and gypsum, and between altered volcanic rocks and volcanic tuffs diagenetically altered to zeolites. However, compared to MSS data, TM data should greatly improve the ability to map hydrothermally altered rocks in arid terrains. ?? 1985.

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

Toward Increasing Teacher Diversity: Targeting Support and Intervention for Teacher Licensure Candidates

ERIC Educational Resources Information Center

Tyler, Linda

2011-01-01

Since 2006, the National Education Association (NEA) and Educational Testing Service (ETS) have been working collaboratively to support teacher candidates in preparing for "The Praxis Series"[TM] of teacher licensure assessments, currently used in 41 states and territories. Their focus has been particularly targeted to assisting minority…

Energy transfer and colour tunability in UV light induced Tm3+/Tb3+/Eu3+: ZnB glasses generating white light emission.

PubMed

Naresh, V; Gupta, Kiran; Parthasaradhi Reddy, C; Ham, Byoung S

2017-03-15

A promising energy transfer (Tm 3+ →Tb 3+ →Eu 3+ ) approach is brought forward to generate white light emission under ultraviolet (UV) light excitation for solid state lightening. Tm 3+ /Tb 3+ /Eu 3+ ions are combinedly doped in zinc borate glass system in view of understanding energy transfer process resulting in white light emission. Zinc borate (host) glass displayed optical and luminescence properties due to formation of Zn(II) x -[O(-II)] y centres in the ZnB glass matrix. At 360nm (UV) excitation, triply doped Tm 3+ /Tb 3+ /Eu 3+ : ZnB glasses simultaneously shown their characteristic emission bands in blue (454nm: 1 D 2 → 3 F 4 ), green (547nm: 5 D 4 → 7 F 5 ) and red (616nm: 5 D 0 → 7 F 2 ) regions. In triple ions doped glasses, energy transfer dynamics is discussed in terms of Forster-Dexter theory, excitation & emission profiles, lifetime curves and from partial energy level diagram of three ions. The role of Tb 3+ in ET from Tm 3+ →Eu 3+ was discussed using branch model. From emission decay analysis, energy transfer probability (P) and efficiency (η) were evaluated. Colour tunability from blue to white on varying (Tb 3+ , Eu 3+ ) content is demonstrated from Commission Internationale de L'Eclairage (CIE) chromaticity coordinates. Based on chromaticity coordinates, other colour related parameters like correlated colour temperature (CCT) and colour purity are also computed for the studied glass samples. An appropriate blending of such combination of rare earth ions could show better suitability as potential candidates in achieving multi-colour and warm/cold white light emission for white LEDs application in the field of solid state lightening. Copyright © 2016 Elsevier B.V. All rights reserved.

Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1)

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

Herlemann, D. P. R.; Geissinger, O.; Ikeda-Ohtsubo, W.

2009-02-01

The candidate phylum Termite group 1 (TG1), is regularly 1 encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191{sup T}, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading tomore » the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a Gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, non-ribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of Elusimicrobia (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.« less

Cnidarian Neurotoxic Peptides Affecting Central Nervous System Targets.

PubMed

Lazcano-Pérez, Fernando; Hernández-Guzmán, Ulises; Sánchez-Rodríguez, Judith; Arreguín-Espinosa, Roberto

2016-01-01

Natural products from animal venoms have been used widely in the discovery of novel molecules with particular biological activities that enable their use as potential drug candidates. The phylum Cnidaria (jellyfish, sea anemones, corals zoanthids, hydrozoans, etc.) is the most ancient venomous phylum on earth. Its venoms are composed of a complex mixture of peptidic compounds with neurotoxic and cytolitic properties that have shown activity on mammalian systems despite the fact that they are naturally targeted against fish and invertebrate preys, mainly crustaceans. For this reason, cnidarian venoms are an interesting and vast source of molecules with a remarkable activity on central nervous system, targeting mainly voltage-gated ion channels, ASIC channels, and TRPV1 receptors. In this brief review, we list the amino acid sequences of most cnidarian neurotoxic peptides reported to date. Additionally, we propose the inclusion of a new type of voltage-gated sea anemone sodium channel toxins based on the most recent reports.

Inhibition of allergic bronchial asthma by thrombomodulin is mediated by dendritic cells.

PubMed

Takagi, Takehiro; Taguchi, Osamu; Toda, Masaaki; Ruiz, Daniel Boveda; Bernabe, Paloma Gil; D'Alessandro-Gabazza, Corina N; Miyake, Yasushi; Kobayashi, Tetsu; Aoki, Shinya; Chiba, Fumiko; Yano, Yutaka; Conway, Edward M; Munesue, Seiichi; Yamamoto, Yasuhiko; Yamamoto, Hiroshi; Suzuki, Koji; Takei, Yoshiyuki; Morser, John; Gabazza, Esteban C

2011-01-01

bronchial asthma is caused by inappropriate acquired immune responses to environmental allergens. It is a major health problem, with a prevalence that is rapidly increasing. Curative therapy is not currently available. to test the hypothesis that thrombomodulin (TM) inhibits allergic bronchial asthma by inducing tolerogenic dendritic cells (DCs). the protective effect of TM was evaluated using a murine asthma model. Asthma was induced in mice by exposure to chicken egg ovalbumin, and the effects of inhaled TM or TM-treated DCs were assessed by administering before ovalbumin exposure. treatment with TM protects against bronchial asthma measured as improved lung function and reduced IgE and cells in alveolar lavage fluid by inducing tolerogenic dendritic dells. These are characterized by high expression of surface TM (CD141/TM(+)) and low expression of maturation markers and possess reduced T-cell costimulatory activity. The CD141/TM(+) DCs migrate less toward chemokines, and after TM treatment there are fewer DCs in the draining lymph node and more in the lungs. The TM effect is independent of its role in coagulation. Rather, it is mediated via the TM lectin domain directly interacting with the DCs. the results of this study show that TM is a modulator of DC immunostimulatory properties and a novel candidate drug for the prevention of bronchial asthma in atopic patients.

Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae.

PubMed

Podosokorskaya, Olga A; Kadnikov, Vitaly V; Gavrilov, Sergey N; Mardanov, Andrey V; Merkel, Alexander Y; Karnachuk, Olga V; Ravin, Nikolay V; Bonch-Osmolovskaya, Elizaveta A; Kublanov, Ilya V

2013-06-01

A novel moderately thermophilic, facultatively anaerobic chemoorganotrophic bacterium strain P3M-2(T) was isolated from a microbial mat developing on the wooden surface of a chute under the flow of hot water (46°C) coming out of a 2775-m-deep oil exploration well (Tomsk region, Russia). Strain P3M-2(T) is a moderate thermophile and facultative anaerobe growing on mono-, di- or polysaccharides by aerobic respiration, fermentation or by reducing diverse electron acceptors [nitrite, Fe(III), As(V)]. Its closest cultivated relative (90.8% rRNA gene sequence identity) is Ignavibacterium album, the only chemoorganotrophic member of the phylum Chlorobi. New genus and species Melioribacter roseus are proposed for isolate P3M-2(T) . Together with I. album, the new organism represents the class Ignavibacteria assigned to the phylum Chlorobi. The revealed group includes a variety of uncultured environmental clones, the 16S rRNA gene sequences of some of which have been previously attributed to the candidate division ZB1. Phylogenetic analysis of M. roseus and I. album based on their 23S rRNA and RecA sequences confirmed that these two organisms could represent an even deeper, phylum-level lineage. Hence, we propose a new phylum Ignavibacteriae within the Bacteroidetes-Chlorobi group with a sole class Ignavibacteria, two families Ignavibacteriaceae and Melioribacteraceae and two species I. album and M. roseus. This proposal correlates with chemotaxonomic data and phenotypic differences of both organisms from other cultured representatives of Chlorobi. The most essential differences, supported by the analyses of complete genomes of both organisms, are motility, facultatively anaerobic and obligately organotrophic mode of life, the absence of chlorosomes and the apparent inability to grow phototrophically. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential.

PubMed

Gruninger, Robert J; Puniya, Anil K; Callaghan, Tony M; Edwards, Joan E; Youssef, Noha; Dagar, Sumit S; Fliegerova, Katerina; Griffith, Gareth W; Forster, Robert; Tsang, Adrian; McAllister, Tim; Elshahed, Mostafa S

2014-10-01

Anaerobic fungi (phylum Neocallimastigomycota) inhabit the gastrointestinal tract of mammalian herbivores, where they play an important role in the degradation of plant material. The Neocallimastigomycota represent the earliest diverging lineage of the zoosporic fungi; however, understanding of the relationships of the different taxa (both genera and species) within this phylum is in need of revision. Issues exist with the current approaches used for their identification and classification, and recent evidence suggests the presence of several novel taxa (potential candidate genera) that remain to be characterised. The life cycle and role of anaerobic fungi has been well characterised in the rumen, but not elsewhere in the ruminant alimentary tract. Greater understanding of the 'resistant' phase(s) of their life cycle is needed, as is study of their role and significance in other herbivores. Biotechnological application of anaerobic fungi, and their highly active cellulolytic and hemi-cellulolytic enzymes, has been a rapidly increasing area of research and development in the last decade. The move towards understanding of anaerobic fungi using -omics based (genomic, transcriptomic and proteomic) approaches is starting to yield valuable insights into the unique cellular processes, evolutionary history, metabolic capabilities and adaptations that exist within the Neocallimastigomycota. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Blue upconversion in Yb3+/Tm3+ co-doped silica fiber based on glass phase-separation technology

NASA Astrophysics Data System (ADS)

Yang, Yu; Chu, Yingbo; Chen, Zhangru; Xing, Yingbin; Hu, Xionwei; Li, Haiqing; Peng, Jinggang; Dai, Nengli; Li, Jinyan; Yang, Luyun

2018-02-01

Yb3+/Tm3+ co-doped silica fiber was prepared successfully by glass phase-separation technology. The measured refractive index profile indicated that the active fiber core had an excellent uniformity. The highest emission intensity was obtained in a sample with a Yb3+ concentration of 0.3 mol/L and a Tm3+ concentration of 0.1 mol/L. Under the excitation at 976 nm, intense blue upconversion emission of Tm3+ at 474 nm was observed due to energy transfer from Yb3+ to Tm3+. A three-photon process was responsible for the blue emission. Due to re-absorption resulted from the Tm3+:3H6→1G4 transition, the blue emission peak was red-shifted. It is suggested that the fiber preparation technology based on glass phase-separation technology can be a potential candidate for preparing active fibers with large core or complex fiber structure.

Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

DOE PAGES

Lin, Qingqing; Li, Huilin; Wang, Tong; ...

2015-04-08

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

Functional reconstitution of the human serotonin receptor 5-HT(6) using synthetic transmembrane peptides.

PubMed

Lee, Won-Kyu; Han, Jason J; Jin, Bong-Suk; Boo, Doo Wan; Yu, Yeon Gyu

2009-12-18

Seven transmembrane (7TM) synthetic peptides mimicking the alpha-helical TM domains of the human serotonin receptor subtype-6 (5-HT(6)) were autonomously reconstituted in detergent micelle and liposome environments. The degree of assembly of the 7TM peptides was characterized by monitoring the fluorescence resonance energy transfer (FRET) between donor and acceptor probes labeled at the amino termini of the second and fourth TM-peptides, respectively. The FRET efficiency of these peptides significantly increased when the 7TM peptides were reconstituted in liposome compare to detergent micelles. Furthermore, the 7TM peptides reconstituted in liposomes selectively bound to free serotonin and serotonin-conjugated magnetic beads, yielding a dissociation constant of 0.84 microM. These results show that the seven individual TM domains of 5-HT(6) can spontaneously assemble into liposomes in a conformation that mimics a native structure, and further demonstrate that specific interactions between TM helices play a critical role in the folding and stabilizing of GPCRs. The autonomous assembly of 7TM-peptides can be applied to the screening of agonists for GPCRs that are difficult to manipulate.

Tunable luminescence mediated by energy transfer in Tm3+/Dy3+ co-doped phosphate glasses under UV excitation

NASA Astrophysics Data System (ADS)

Chen, Yong; Chen, Guohua; Liu, Xiangyu; Yuan, Changlai; Zhou, Changrong

2017-11-01

Tm3+/Dy3+ co-doped phosphate glasses for white light-emitting diodes were synthesized by a conventional melting-quenching method. A spectroscopic research based on optical, photoluminescence spectrum and decay time curves in Tm3+/Dy3+ co-doped phosphate glasses was carried out. The color of luminescence could be tuned by altering the concentrations of Tm3+ ions. Under UV light excitation, the CIE chromaticity coordinates (0.3471, 0.3374) and color correlate temperature (CCT = 4866.21 K) close to the standard white-light illumination (0.333, 0.333 and CCT = 5454.12 K) could be achieved in 0.4 Tm3+/0.6 Dy3+ (mol %) co-doped glass sample. The decrease of the Dy3+ emission decay time in existence of Tm3+ ascertained that non-radiative energy transfer from Dy3+ to Tm3+ occurred. Moreover, the research of energy transfers between Dy3+ and Tm3+ based on the Inokuti-Hirayama model revealed that an electric quadrupole-quadrupole interaction might be the predominant mechanism participated in the energy transfer. This finding suggests that the as-prepared Tm3+/Dy3+ co-doped phosphate glasses may be promising candidate for white LEDs and other display devices.

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

PubMed Central

Chiang, Edna; Schmidt, Marian L.; Berry, Michelle A.; Biddanda, Bopaiah A.; Burtner, Ashley; Johengen, Thomas H.; Palladino, Danna

2018-01-01

The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7–41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia. PMID:29590198

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

PubMed Central

Wrighton, Kelly C; Castelle, Cindy J; Wilkins, Michael J; Hug, Laura A; Sharon, Itai; Thomas, Brian C; Handley, Kim M; Mullin, Sean W; Nicora, Carrie D; Singh, Andrea; Lipton, Mary S; Long, Philip E; Williams, Kenneth H; Banfield, Jillian F

2014-01-01

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling. PMID:24621521

Combinatorial Search for High-Activity Hydrogen Catalysts Based on Transition-Metal-Embedded Graphitic Carbons

DOE PAGES

Choi, Woon Ih; Wood, Brandon C.; Schwegler, Eric; ...

2015-09-22

Transition metal (TM) atoms in porphyrin–like complexes play important roles in many protein and enzymetic systems, where crystal–field effects are used to modify d–orbital levels. Inspired by the tunable electronic structure of these motifs, a high–throughput computational search for synthetic hydrogen catalysts is performed based on a similar motif of TM atoms embedded into the lattice of graphene. Based on an initial list of 300 possible embedding geometries, binders, and host atoms, descriptors for stability and catalytic activity are applied to extract ten promising candidates for hydrogen evolution, two of which are expected to exhibit high activity for hydrogen oxidation.more » In several instances, the active TM atoms are earth–abundant elements that show no activity in the bulk phase, highlighting the importance of the coordination environment in tuning the d–orbitals. In conclusion, it is found that the most active candidates involve a hitherto unreported surface reaction pathway that involves a Kubas–complex intermediate, which significantly lowers the kinetic barrier associated with hydrogen dissociation and association.« less

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

PubMed Central

Kamke, Janine; Sczyrba, Alexander; Ivanova, Natalia; Schwientek, Patrick; Rinke, Christian; Mavromatis, Kostas; Woyke, Tanja; Hentschel, Ute

2013-01-01

Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems. PMID:23842652

Microbial Community Analysis of Anaerobic Reactors Treating Soft Drink Wastewater

PubMed Central

Narihiro, Takashi; Kim, Na-Kyung; Mei, Ran; Nobu, Masaru K.; Liu, Wen-Tso

2015-01-01

The anaerobic packed-bed (AP) and hybrid packed-bed (HP) reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG) and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95%) after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs). Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR) increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR. PMID:25748027

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

PubMed Central

Becraft, Eric D.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.; Ohlsson, J. Ingemar; Briggs, Brandon R.; Kanbar, Jad; De Vlaminck, Iwijn; Quake, Stephen R.; Dong, Hailiang; Hedlund, Brian P.

2015-01-01

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This “microbial dark matter” represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum “Calescamantes” (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs. PMID:26637598

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls.

PubMed

Zhou, Zhenming; Meng, Qingxiang; Li, Shengli; Jiang, Lan; Wu, Hao

2017-08-01

In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME = 11.3 MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P > 0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P = 0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P = 0.0092 and P = 0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P = 0.0299 and P = 0.0007, respectively) and decreased the abundance of vadinCA11 (P = 0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.

Possibility of a ferromagnetic and conducting metal-organic network

NASA Astrophysics Data System (ADS)

Mabrouk, Manel; Hayn, Roland; Denawi, Hassan; Ben Chaabane, Rafik

2018-05-01

In this paper, we present first principles calculations based on the spin-polarized generalized gradient approximation with on-site Coulomb repulsion term (SGGA + U), to explore the electronic and magnetic properties of the novel planar metal-organic networks TM-Pc and TM-TCNB (where TM means a transition metal of the 3d series: Ti, V, Cr, …, or Zn, Pc - Phthalocyanine, and TCNB - Tetracyanobenzene) as free-standing sheets. This work is an extension of two earlier research works dealing with the Mn (Mabrouk et al., 2015) and Fe (Mabrouk et al., 2017) cases. Our theoretical investigations demonstrate that TM-Pc are more stable than TM-TCNB. Our results unveil that all the TM-Pc frameworks have an insulating behavior with the exception of Mn-Pc which is half-metallic and favor antiferromagnetic order in the case of our magnetic systems except for V-Pc which is ferromagnetic. In contrast, the TM-TCNB networks are metallic at least in one spin direction and exhibit long-range ferromagnetic coupling in case for magnetic structures, which represent ideal candidates and an interesting prospect of unprecedented applications in spintronics. In addition, these results may shed light to achieve a new pathway on further experimental research in molecular spintronics.

Differential Protein Expression Profiles in Glaucomatous Trabecular Meshwork: An Evaluation Study on a Small Primary Open Angle Glaucoma Population.

PubMed

Micera, Alessandra; Quaranta, Luciano; Esposito, Graziana; Floriani, Irene; Pocobelli, Augusto; Saccà, Sergio Claudio; Riva, Ivano; Manni, Gianluca; Oddone, Francesco

2016-02-01

Primary open angle glaucoma (POAG) is a progressive optic neuropathy characterized by impaired aqueous outflow and extensive remodeling in the trabecular meshwork (TM). The aim of this study was to characterize and compare the expression patterns of selected proteins belonging to the tissue remodeling, inflammation and growth factor pathways in ex vivo glaucomatous and post-mortem TMs using protein-array analysis. TM specimens were collected from 63 white subjects, including 40 patients with glaucoma and 23 controls. Forty POAG TMs were collected at the time of surgery and 23 post-mortem specimens were from non-glaucomatous donor sclerocorneal tissues. Protein profiles were evaluated using a chip-based array consisting of 60 literature-selected antibodies. A different expression of some factors was observed in POAG TMs with respect to post-mortem specimens, either in abundance (interleukin [IL]10, IL6, IL5, IL7, IL12, IL3, macrophage inflammatory protein [MIP]1δ/α, vascular endothelial growth factor [VEGF], transforming growth factor beta 1 [TGFβ1], soluble tumor necrosis factor receptor I [sTNFRI]) or in scarcity (IL16, IL18, intercellular adhesion molecule 3 [ICAM3], matrix metalloproteinase-7 [MMP7], tissue inhibitor of metalloproteinase 1 [TIMP1]). MMP2, MMP7, TGFβ1, and VEGF expressions were confirmed by Western blot, zymography, and polymerase chain reaction. No difference in protein profile expression was detected between glaucomatous subtypes. The analysis of this small TM population highlighted some proteins linked to POAG, some previously reported and others of new detection (IL7, MIPs, sTNFαRI). A larger POAG population is required to select promising disease-associated biomarker candidates. This study was partially supported by the Fondazione Roma, the Italian Ministry of Health and the "National 5xMille 2010 tax donation to IRCCS-G.B. Bietti Foundation".

Anaerobic transformation of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) by ovine rumen microorganisms.

PubMed

Perumbakkam, Sudeep; Craig, A M

2012-01-01

Explosives such as octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) provide a challenge in terms of bioremediation. In the present study, sheep rumen was studied for its potential to detoxify HMX using analytical chemistry and molecular microbial ecology tools. Results indicated significant loss (p < 0.05) of HMX at 8 h post-incubation and complete disappearance of the parent molecule after 16 h. Qualitative LC-MS/MS analysis provided evidence for the formation of 1-NO-HMX and MEDINA metabolites. A total of 1006 16S rRNA-V3 clones were sequenced and the Classifier tool of the RDPII database was used to sort the sequences at their phylum level. Most sequences were associated with either the phylum Bacteroidetes or Firmicutes. Significant differences at the phylum level (p < 0.001) were found between 0 h and 8 h HMX treatments. Using LibCompare analysis, 8 h HMX treatment showed enrichment of clones (p < 0.01) belonging to the genus Prevotella. From these results, it could be concluded that members of the genus Prevotella are enriched in the rumen and are capable of detoxifying HMX. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

A Comparative Study of QD and Nitrogen-Based 1.3 mu m VCSELs

DTIC Science & Technology

2001-06-01

molecular beam epitaxy (MBE) proposed as promising candidates for 1.3 /tm emitters. Among them InGaAsN quantum well (QW) and InGaAs quantum dots (QD... VCSELs DISTRIBUTION: Approved for public release, distribution unlimited Availability: Hard copy only. This paper is part of the following report: TITLE...and Technology" LOED.02 St Petersburg, Russia, June 18-22, 2001 ©0 2001 loffe Institute A comparative study of QD and nitrogen-based 1.3 /tm VCSELs A. P

A Novel Mgp-Cre Knock-In Mouse Reveals an Anticalcification/Antistiffness Candidate Gene in the Trabecular Meshwork and Peripapillary Scleral Region.

PubMed

Borrás, Teresa; Smith, Matthew H; Buie, LaKisha K

2015-04-01

Soft tissue calcification is a pathological condition. Matrix Gla (MGP) is a potent mineralization inhibitor secreted by cartilage chondrocytes and arteries' vascular smooth muscle cells. Mgp knock-out mice die at 6 weeks due to massive arterial calcification. Arterial calcification results in arterial stiffness and higher systolic blood pressure. Intriguingly, MGP was highly abundant in trabecular meshwork (TM). Because tissue stiffness is relevant to glaucoma, we investigated which additional eye tissues use Mgp's function using knock-in mice. An Mgp-Cre-recombinase coding sequence (Cre) knock-in mouse, containing Mgp DNA plus an internal ribosomal entry site (IRES)-Cre-cassette was generated by homologous recombination. Founders were crossed with Cre-mediated reporter mouse R26R-lacZ. Their offspring expresses lacZ where Mgp is transcribed. Eyes from MgpCre/+;R26RlacZ/+ (Mgp-lacZ knock-in) and controls, 1 to 8 months were assayed for β-gal enzyme histochemistry. As expected, Mgp-lacZ knock-in's TM was intensely blue. In addition, this mouse revealed high specific expression in the sclera, particularly in the peripapillary scleral region (ppSC). Ciliary muscle and sclera above the TM were also positive. Scleral staining was located immediately underneath the choroid (chondrocyte layer), began midsclera and was remarkably high in the ppSC. Cornea, iris, lens, ciliary body, and retina were negative. All mice exhibited similar staining patterns. All controls were negative. Matrix Gla's restricted expression to glaucoma-associated tissues from anterior and posterior segments suggests its involvement in the development of the disease. Matrix Gla's anticalcification/antistiffness properties in the vascular tissue, together with its high TM and ppCS expression, place this gene as a strong candidate for TM's softness and sclera's stiffness regulation in glaucoma.

Combined effects of the PNPLA3 rs738409, TM6SF2 rs58542926, and MBOAT7 rs641738 variants on NAFLD severity: a multicenter biopsy-based study1[S

PubMed Central

Krawczyk, Marcin; Rau, Monika; Schattenberg, Jörn M.; Bantel, Heike; Pathil, Anita; Demir, Münevver; Kluwe, Johannes; Boettler, Tobias; Lammert, Frank; Geier, Andreas

2017-01-01

The PNPLA3 p.I148M, TM6SF2 p.E167K, and MBOAT7 rs641738 variants represent genetic risk factors for nonalcoholic fatty liver disease (NAFLD). Here we investigate if these polymorphisms modulate both steatosis and fibrosis in patients with NAFLD. We recruited 515 patients with NAFLD (age 16–88 years, 280 female patients). Liver biopsies were performed in 320 patients. PCR-based assays were used to genotype the PNPLA3, TM6SF2, and MBOAT7 variants. Carriers of the PNPLA3 and TM6SF2 risk alleles showed increased serum aspartate aminotransferase and alanine transaminase activities (P < 0.05). The PNPLA3 genotype was associated with steatosis grades S2–S3 (P < 0.001) and fibrosis stages F2–F4 (P < 0.001). The TM6SF2 genotype was associated with steatosis (P = 0.003) but not with fibrosis (P > 0.05). The MBOAT7 variant was solely associated with increased fibrosis (P = 0.046). In the multivariate model, variants PNPLA3 (P = 0.004) and TM6SF2 (P = 0.038) were associated with steatosis. Fibrosis stages were affected by the PNPLA3 (P = 0.042) and MBOAT7 (P = 0.021) but not by the TM6SF2 polymorphism (P > 0.05). The PNPLA3, TM6SF2, and MBOAT7 variants are associated with increased liver injury. The TM6SF2 variant seems to modulate predominantly hepatic fat accumulation, whereas the MBOAT7 polymorphism is linked to fibrosis. The PNPLA3 polymorphism confers risk of both increased steatosis and fibrosis. PMID:27836992

Combined effects of the PNPLA3 rs738409, TM6SF2 rs58542926, and MBOAT7 rs641738 variants on NAFLD severity: a multicenter biopsy-based study.

PubMed

Krawczyk, Marcin; Rau, Monika; Schattenberg, Jörn M; Bantel, Heike; Pathil, Anita; Demir, Münevver; Kluwe, Johannes; Boettler, Tobias; Lammert, Frank; Geier, Andreas

2017-01-01

The PNPLA3 p.I148M, TM6SF2 p.E167K, and MBOAT7 rs641738 variants represent genetic risk factors for nonalcoholic fatty liver disease (NAFLD). Here we investigate if these polymorphisms modulate both steatosis and fibrosis in patients with NAFLD. We recruited 515 patients with NAFLD (age 16-88 years, 280 female patients). Liver biopsies were performed in 320 patients. PCR-based assays were used to genotype the PNPLA3, TM6SF2, and MBOAT7 variants. Carriers of the PNPLA3 and TM6SF2 risk alleles showed increased serum aspartate aminotransferase and alanine transaminase activities (P < 0.05). The PNPLA3 genotype was associated with steatosis grades S2-S3 (P < 0.001) and fibrosis stages F2-F4 (P < 0.001). The TM6SF2 genotype was associated with steatosis (P = 0.003) but not with fibrosis (P > 0.05). The MBOAT7 variant was solely associated with increased fibrosis (P = 0.046). In the multivariate model, variants PNPLA3 (P = 0.004) and TM6SF2 (P = 0.038) were associated with steatosis. Fibrosis stages were affected by the PNPLA3 (P = 0.042) and MBOAT7 (P = 0.021) but not by the TM6SF2 polymorphism (P > 0.05). The PNPLA3, TM6SF2, and MBOAT7 variants are associated with increased liver injury. The TM6SF2 variant seems to modulate predominantly hepatic fat accumulation, whereas the MBOAT7 polymorphism is linked to fibrosis. The PNPLA3 polymorphism confers risk of both increased steatosis and fibrosis. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Comparative assessment of the bacterial communities associated with Aedes aegypti larvae and water from domestic water storage containers.

PubMed

Dada, Nsa; Jumas-Bilak, Estelle; Manguin, Sylvie; Seidu, Razak; Stenström, Thor-Axel; Overgaard, Hans J

2014-08-24

Domestic water storage containers constitute major Aedes aegypti breeding sites. We present for the first time a comparative analysis of the bacterial communities associated with Ae. aegypti larvae and water from domestic water containers. The 16S rRNA-temporal temperature gradient gel electrophoresis (TTGE) was used to identify and compare bacterial communities in fourth-instar Ae. aegypti larvae and water from larvae positive and negative domestic containers in a rural village in northeastern Thailand. Water samples were cultured for enteric bacteria in addition to TTGE. Sequences obtained from TTGE and bacterial cultures were clustered into operational taxonomic units (OTUs) for analyses. Significantly lower OTU abundance was found in fourth-instar Ae. aegypti larvae compared to mosquito positive water samples. There was no significant difference in OTU abundance between larvae and mosquito negative water samples or between mosquito positive and negative water samples. Larval samples had significantly different OTU diversity compared to mosquito positive and negative water samples, with no significant difference between mosquito positive and negative water samples. The TTGE identified 24 bacterial taxa, belonging to the phyla Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and TM7 (candidate phylum). Seven of these taxa were identified in larval samples, 16 in mosquito positive and 13 in mosquito negative water samples. Only two taxa, belonging to the phyla Firmicutes and Actinobacteria, were common to both larvae and water samples. Bacilli was the most abundant bacterial class identified from Ae. aegypti larvae, Gammaproteobacteria from mosquito positive water samples, and Flavobacteria from mosquito negative water samples. Enteric bacteria belonging to the class Gammaproteobacteria were sparsely represented in TTGE, but were isolated from both mosquito positive and negative water samples by selective culture. Few bacteria from water samples were identified in fourth-instar Ae. aegypti larvae, suggesting that established larval bacteria, most likely acquired at earlier stages of development, control the larval microbiota. Further studies at all larval stages are needed to fully understand the dynamics involved. Isolation of enteric bacteria from water samples supports earlier outcomes of E. coli contamination in Ae. aegypti infested domestic containers, suggesting the need to further explore the role of enteric bacteria in Ae. aegypti infestation.

GPR30: a seven-transmembrane-spanning estrogen receptor that triggers EGF release.

PubMed

Filardo, Edward J; Thomas, Peter

2005-10-01

Heterotrimeric G proteins and seven-transmembrane-spanning (7TM) receptors are implicated in rapid estrogen signaling. The orphan 7TM receptor GPR30 is linked to estrogen-mediated activation of adenylyl cyclase, release of epidermal growth factor (EGF)-related ligands, and specific estrogen binding. GPR30 acts independently of estrogen receptors, ERalpha and ERbeta, and probably functions as a heptahelical ER. 7TM receptors elicit signals that stimulate second messengers, and convey intracellular signals via EGF receptors. Identification of GPR30 as a Gs-coupled 7TM receptor that triggers release of heparin-binding EGF establishes its role in cell signaling cascades initiated by estrogens, and explains their capacity to activate second messengers and promote EGF-like effects. Thus, estrogen can signal by the same mechanism as various other hormones, through a specific 7TM receptor.

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

DOE PAGES

Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

2014-11-05

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islandsmore » in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.« less

Tamm-plasmon and surface-plasmon hybrid-mode based refractometry in photonic bandgap structures.

PubMed

Das, Ritwick; Srivastava, Triranjita; Jha, Rajan

2014-02-15

The transverse magnetic (TM) polarized hybrid modes formed as a consequence of coupling between Tamm plasmon polariton (TM-TPP) mode and surface plasmon polariton (SPP) mode exhibit interesting dispersive features for realizing a highly sensitive and accurate surface plasmon resonance (SPR) sensor. We found that the TM-TPP modes, formed at the interface of distributed Bragg reflector and metal, are strongly dispersive as compared to SPP modes at optical frequencies. This causes an appreciably narrow interaction bandwidth between TM-TPP and SPP modes, which leads to highly accurate sensing. In addition, appropriate tailoring of dispersion characteristics of TM-TPP as well as SPP modes could ensure high sensitivity of a novel SPR platform. By suitably designing the Au/TiO₂/SiO₂-based geometry, we propose a TM-TPP/SPP hybrid-mode sensor and achieve a sensitivity ≥900  nm/RIU with high detection accuracy (≥30  μm⁻¹) for analyte refractive indices varying between 1.330 and 1.345 in 600-700 nm wavelength range. The possibility to achieve desired dispersive behavior in any spectral band makes the sensing configuration an extremely attractive candidate to design sensors depending on the availability of optical sources.

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Briggs, Brandon R.; Peacock, Joseph P.; Huang, Qiuyuan; Huang, Liuqin; Wu, Geng; Zhi, Xiaoyang; Li, Wenjun; Dodsworth, Jeremy A.; Hedlund, Brian P.; Zhang, Chuanlun; Hartnett, Hilairy E.; Dijkstra, Paul; Hungate, Bruce A.

2013-01-01

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world. PMID:23326417

A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing.

PubMed

Hou, Weiguo; Wang, Shang; Dong, Hailiang; Jiang, Hongchen; Briggs, Brandon R; Peacock, Joseph P; Huang, Qiuyuan; Huang, Liuqin; Wu, Geng; Zhi, Xiaoyang; Li, Wenjun; Dodsworth, Jeremy A; Hedlund, Brian P; Zhang, Chuanlun; Hartnett, Hilairy E; Dijkstra, Paul; Hungate, Bruce A

2013-01-01

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21-123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5-2.6), high temperature (85.1-89.1°C), and high sulfur contents favored the crenarchaeal order Sulfolobales, whereas those with low pH (2.6-4.8) and cooler temperature (55.1-64.5°C) favored the Aquificae genus Hydrogenobaculum. Rehai springs with neutral-alkaline pH (7.2-9.4) and high temperature (>80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Desulfurococcales and Thermoproteales became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single Aquificae genus Hydrogenobacter, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon "Candidatus Nitrosocaldus yellowstonii", and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

The separation of Gln and Glu in STEAM: a comparison study using short and long TEs/TMs at 3 and 7 T.

PubMed

Dou, Weiqiang; Kaufmann, Jörn; Li, Meng; Zhong, Kai; Walter, Martin; Speck, Oliver

2015-08-01

This study aimed to determine the optimal echo time (TE) and mixing time (TM) for in vivo glutamine (Gln) and glutamate (Glu) separation in stimulated-echo acquisition mode at 3 and 7 T. We applied a short TE/TM (20/10 ms) for a high signal-to-noise-ratio and a field-specific long TE/TM (3 T: 72/6 ms; 7 T: 74/68 ms) for optimal Gln and Glu separation of the Carbon-4 proton resonances. Corresponding Gln and Glu spectra were simulated using VeSPA software, and measured in a phantom and human brains at 3 and 7 T. Higher spectral separation for Gln and Glu was achieved at 7 than 3 T. At 7 T, short TE/TM provided comparable spectral separation and in vitro Gln and Glu quantification compared to long TE/TM. Moreover, it showed greater reliability in in vivo Gln and Glu detection and separation than long TE/TM, with significantly lower Cramer-Rao lower bounds (Gln: 14.9 vs. 75.8; Glu: 3.8 vs. 6.5) and correlation between Gln and Glu (p = 0.004). Based on the optimal separation for Gln and Glu, a short TE/TM at 7 T is proposed for future in vivo Gln and Glu acquisition.

NMR Investigation of Structures of G-protein Coupled Receptor Folding Intermediates*

PubMed Central

Poms, Martin; Ansorge, Philipp; Martinez-Gil, Luis; Jurt, Simon; Gottstein, Daniel; Fracchiolla, Katrina E.; Cohen, Leah S.; Güntert, Peter; Mingarro, Ismael; Naider, Fred; Zerbe, Oliver

2016-01-01

Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot, J. L., and Engelman, D. M. (1990) Biochemistry 29, 4031–4037) is postulated to proceed in 2 steps: partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two, and the first three transmembrane (TM) segments, as well as a construct comprising TM1–TM2 covalently linked to TM7 were examined. We observed that the isolated TM1 does not form a stable helix nor does it integrate well into the micelle. TM1 is significantly stabilized upon interaction with TM2, forming a helical hairpin reported previously (Neumoin, A., Cohen, L. S., Arshava, B., Tantry, S., Becker, J. M., Zerbe, O., and Naider, F. (2009) Biophys. J. 96, 3187–3196), and in this case the protein integrates into the hydrophobic interior of the micelle. TM123 displays a strong tendency to oligomerize, but hydrogen exchange data reveal that the center of TM3 is solvent exposed. In all GPCRs so-far structurally characterized TM7 forms many contacts with TM1 and TM2. In our study TM127 integrates well into the hydrophobic environment, but TM7 does not stably pack against the remaining helices. Topology mapping in microsomal membranes also indicates that TM1 does not integrate in a membrane-spanning fashion, but that TM12, TM123, and TM127 adopt predominantly native-like topologies. The data from our study would be consistent with the retention of individual helices of incompletely synthesized GPCRs in the vicinity of the translocon until the complete receptor is released into the membrane interior. PMID:27864365

Superstrong Adjustable Permanent Magnet for a Linear Collider Final Focus

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

Mihara, T.

A superstrong permanent magnet quadrupole (PMQ) is one of the candidates for the final focus lens for the linear collider because of its compactness and low power consumption. The first fabricated prototype of our PMQ achieved a 300T/m superstrong field gradient with a 100mm overall magnet radius and a 7mm bore radius, but a drawback is its fixed strength. Therefore, a second prototype of PMQ, whose strength is adjustable, was fabricated. Its strength adjustability is based on the ''double ring structure'', rotating subdivided magnet slices separately. This second prototype is being tested. Some of the early results are presented.

Pilot Study of Sublethal Effects on Fish of Pesticides Currently Used and Proposed for Use on Maine Blueberries

USGS Publications Warehouse

Elskus, Adria A.

2007-01-01

Blueberry pesticides have been detected consistently in some Down East Maine rivers, yet little is known about the sublethal effects of these pesticides on fish early life stages. The Maine blueberry industry is proposing to replace the insecticide ImidanTM (active ingredient phosmet) and the herbicide VelparTM (active ingredient hexazinone), two of the pesticides found in these rivers, with candidate alternatives SpinTor TM (active ingredient spinosad) and Callistso TM (active ingredient mesotrione). Our objective is to evaluate potential sublethal effects of these four formulations before the industry adopts the two candidate alternatives. We exposed zebrafish (Danio rerio) early life stages, from fertilization through larval swim-up, to a range of pesticide concentrations and evaluated their response relative to untreated controls. In this report we provide preliminary data on immune function as well as on parameters in addition to those originally proposed: development and performance fitness. We also provide information on our progress towards optimizing chemical protocols for analyzing the concentration of active ingredient in each of our formulation dosing solutions, another new parameter we added to those originally proposed. Preliminary results indicate that at environmentally realistic concentrations, these pesticides may have no significant effect on innate immunity, development rate or behavior (spontaneous swimming), however further replication is needed to confirm these initial findings. We have also observed some degree of developmental abnormalities in both pesticide-treated and control zebrafish embryos; however, additional replication is underway to determine if these groups differ significantly.

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes.

PubMed

Becraft, Eric D; Dodsworth, Jeremy A; Murugapiran, Senthil K; Ohlsson, J Ingemar; Briggs, Brandon R; Kanbar, Jad; De Vlaminck, Iwijn; Quake, Stephen R; Dong, Hailiang; Hedlund, Brian P; Swingley, Wesley D

2016-02-15

The vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. This "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. In this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "Calescamantes" (EM19) to calibrate machine learning algorithms and define metagenomic bins directly from pyrosequencing reads derived from Great Boiling Spring in the U.S. Great Basin. Compared to other assembly-based methods, taxonomic binning with a read-based machine learning approach yielded final assemblies with the highest predicted genome completeness of any method tested. Read-first binning subsequently was used to extract Calescamantes bins from all metagenomes with abundant Calescamantes populations, including metagenomes from Octopus Spring and Bison Pool in Yellowstone National Park and Gongxiaoshe Spring in Yunnan Province, China. Metabolic reconstruction suggests that Calescamantes are heterotrophic, facultative anaerobes, which can utilize oxidized nitrogen sources as terminal electron acceptors for respiration in the absence of oxygen and use proteins as their primary carbon source. Despite their phylogenetic divergence, the geographically separate Calescamantes populations were highly similar in their predicted metabolic capabilities and core gene content, respiring O2, or oxidized nitrogen species for energy conservation in distant but chemically similar hot springs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring.

PubMed

Díaz-Cárdenas, C; López, G; Patel, B K C; Baena, S

2010-04-01

A mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82(T), was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5-7 x 1.3 microm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 degrees C (growth range 20-40 degrees C), pH 7.3 (growth range pH 5.5-8.5) and 2 % (w/v) NaCl (growth range 0.1-7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain USBA 82(T) was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82(T) represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82(T) (=DSM 21565(T)=KCTC 5659(T)).

Direct-Acting Antiviral Therapy Outcomes in Canadian Chronic Hepatitis C Telemedicine Patients.

PubMed

Cooper, Curtis L; Hatashita, Holly; Corsi, Daniel J; Parmar, Parmvir; Corrin, Raymond; Garber, Gary

Many of the 300,000 HCV-infected Canadians live in under-served and remote areas without access to HCV healthcare specialists. Telemedicine (TM) and advances in HCV management can facilitate linkage of these marginalized patients to healthcare. A cohort database analysis was performed on patients followed at The Ottawa Hospital and Regional Viral Hepatitis Program between January 2012 and August 2016. We compared patient characteristics, fibrosis work-up and antiviral treatment outcomes in TM (n = 157) and non-TM (n = 1,130) patients (The Ottawa Hospital Viral Hepatitis Outpatient Clinic) residing in Eastern Ontario. TM patients were more often infected with genotype 3 (25.9% vs. 16.4%), were more commonly Indigenous (7.0% vs. 2.2%) had a history of injection drug use (70.1% vs. 54.9%) and incarceration (46.5% vs 35.5%). Groups were comparable in age (48.9 years), gender (63.7% male) and cirrhotic stage (24.0%). 59.2% of TM patients underwent transient elastography during regional outreach blitzes compared to 61.8% of non-TM patients (p = 0.54). Overall, half as many TM patients initiated antiviral therapy as non-TM patients (27.4% vs. 53.8%, p < 0.001). The introduction of DAA regimens is bridging this gap (22.2% of TM patients vs. 34.3% of non-TM patients). SVR rates with interferon-free, DAA regimens were 94.7% and 94.8% in TM and non-TM groups (p = 0.99). Our TM program engages and retains a population that faces many barriers to effective HCV treatment. TM patients initiated HCV therapy and achieved High SVR rates comparable to those obtained using traditional models of care.

Low glucose level and low pH alter the electrochemical function of human parietal pleura.

PubMed

Kouritas, V K; Hatzoglou, C; Foroulis, C N; Hevas, A; Gourgoulianis, K I; Molyvdas, P A

2007-08-01

The aim of the present study was to investigate whether low glucose and pH level, which are usually measured in complicated pleural effusions, alter the electrochemical function of healthy human parietal pleura. Parietal pleural pieces were stripped from 66 patients during thoracic surgery and were mounted in Ussing chambers. Krebs' solutions containing different glucose levels (0, 40 and 100 mg) and balanced at different pH levels (7.4, 7.3 and 7.2) were added to the pleural cavity surface of the pieces. Transmesothelial potential difference was measured at various time-points as an electrophysiological variable and transmesothelial resistance (R(TM)) was calculated using Ohm's law. When normal-glucose Krebs at pH 7.45 was used, R(TM) remained unchanged over time, but when low-glucose Krebs was used, R(TM) decreased. Krebs without glucose caused the greatest decrease in R(TM). Use of low-pH Krebs decreased R(TM). The lower the pH of the Krebs, the faster the decrease in R(TM) and the greater the effect. The decrease in R(TM) was greater with low-pH than with low-glucose Krebs. Low glucose and low pH caused an additive decrease in R(TM). Low glucose concentration and low pH cause alteration of the electrochemical function of human parietal pleura and could act as agents that lead to further exudate progression.

Improvement in absolute calibration accuracy of Landsat-5 TM with Landsat-7 ETM+ data

USGS Publications Warehouse

Chander, G.; Markham, B.L.; Micijevic, E.; Teillet, P.M.; Helder, D.L.; ,

2005-01-01

The ability to detect and quantify changes in the Earth's environment depends on satellites sensors that can provide calibrated, consistent measurements of Earth's surface features through time. A critical step in this process is to put image data from subsequent generations of sensors onto a common radiometric scale. To evaluate Landsat-5 (L5) Thematic Mapper's (TM) utility in this role, image pairs from the L5 TM and Landsat-7 (L7) Enhanced Thematic Mapper Plus (ETM+) sensors were compared. This approach involves comparison of surface observations based on image statistics from large common areas observed eight days apart by the two sensors. The results indicate a significant improvement in the consistency of L5 TM data with respect to L7 ETM+ data, achieved using a revised Look-Up-Table (LUT) procedure as opposed to the historical Internal Calibrator (IC) procedure previously used in the L5 TM product generation system. The average percent difference in reflectance estimates obtained from the L5 TM agree with those from the L7 ETM+ in the Visible and Near Infrared (VNIR) bands to within four percent and in the Short Wave Infrared (SWIR) bands to within six percent.

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs.

PubMed

Macfarlane, J M; Lambe, N R; Matika, O; Johnson, P L; Wolf, B T; Haresign, W; Bishop, S C; Bünger, L

2014-07-01

TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (P<0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/+ than +/+ lambs (-11.2%; P<0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm

PubMed Central

Oliveira, R.R.D.S.; Fermiano, D.; Feres, M.; Figueiredo, L.C.; Teles, F.R.F.; Soares, G.M.S.; Faveri, M.

2016-01-01

In recent years, several new periodontal taxa have been associated with the etiology of periodontitis. A recent systematic review provides further support for the pathogenic role of 17 species/phylotypes. Thus, the aim of this study was to assess the prevalence and levels of these species in subjects with generalized chronic periodontitis (GChP; n = 30), generalized aggressive periodontitis (GAgP; n = 30), and periodontal health (PH; n = 30). All subjects underwent clinical and microbiological assessment. Nine subgingival plaque samples were collected from each subject and analyzed for their content of 20 bacterial species/phylotypes through the RNA-oligonucleotide quantification technique. Subjects from the GChP and GAgP groups presented the highest mean values for all clinical parameters in comparison with the PH group (P < 0.05). Subjects with GChP and GAgP showed significantly higher mean levels of Bacteroidetes sp. human oral taxon (HOT) 274, Fretibacterium sp. HOT 360, and TM7 sp. HOT 356 phylotypes, as well as higher mean levels of Filifactor alocis, Fretibacterium fastidiosum, Porphyromonas gingivalis, Tannerella forsythia, and Selenomonas sputigena species than PH subjects (P < 0.05). GAgP subjects presented higher mean levels of TM7 sp. HOT 356 and F. alocis than GChP subjects (P < 0.05). A significantly higher mean prevalence of Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, and Fretibacterium sp. HOT 362 was found in subjects with GChP and GAgP than in PH subjects. Mean levels of P. gingivalis (r = 0.68), T. forsythia (r = 0.62), F. alocis (r = 0.51, P = 0.001), and Fretibacterium sp. HOT 360 (r = 0.41) were correlated with pocket depth (P < 0.001). In conclusion, Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, Fretibacterium sp. HOT 362, and TM7 sp. HOT 356 phylotypes, in addition to F. alocis, F. fastidiosum, and S. sputigena, seem to be associated with periodontitis, and their role in periodontal pathogenesis should be further investigated. PMID:26936213

The Sloan Lens ACS Survey. XIII. Discovery of 40 New Galaxy-scale Strong Lenses

NASA Astrophysics Data System (ADS)

Shu, Yiping; Brownstein, Joel R.; Bolton, Adam S.; Koopmans, Léon V. E.; Treu, Tommaso; Montero-Dorta, Antonio D.; Auger, Matthew W.; Czoske, Oliver; Gavazzi, Raphaël; Marshall, Philip J.; Moustakas, Leonidas A.

2017-12-01

We present the full sample of 118 galaxy-scale strong-lens candidates in the Sloan Lens ACS (SLACS) Survey for the Masses (S4TM) Survey, which are spectroscopically selected from the final data release of the Sloan Digital Sky Survey. Follow-up Hubble Space Telescope (HST) imaging observations confirm that 40 candidates are definite strong lenses with multiple lensed images. The foreground-lens galaxies are found to be early-type galaxies (ETGs) at redshifts 0.06–0.44, and background sources are emission-line galaxies at redshifts 0.22–1.29. As an extension of the SLACS Survey, the S4TM Survey is the first attempt to preferentially search for strong-lens systems with relatively lower lens masses than those in the pre-existing strong-lens samples. By fitting HST data with a singular isothermal ellipsoid model, we find that the total projected mass within the Einstein radius of the S4TM strong-lens sample ranges from 3 × 1010 M ⊙ to 2 × 1011 M ⊙. In Shu et al., we have derived the total stellar mass of the S4TM lenses to be 5 × 1010 M ⊙ to 1 × 1012 M ⊙. Both the total enclosed mass and stellar mass of the S4TM lenses are on average almost a factor of 2 smaller than those of the SLACS lenses, which also represent the typical mass scales of the current strong-lens samples. The extended mass coverage provided by the S4TM sample can enable a direct test, with the aid of strong lensing, for transitions in scaling relations, kinematic properties, mass structure, and dark-matter content trends of ETGs at intermediate-mass scales as noted in previous studies. Based on observations made with the NASA/ESA Hubble Space Telescope (HST), obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555. These observations are associated with HST program #12210.

Influence of prognostic nutritional index and tumor markers on survival in gastric cancer surgery patients.

PubMed

Saito, Hiroaki; Kono, Yusuke; Murakami, Yuki; Kuroda, Hirohiko; Matsunaga, Tomoyuki; Fukumoto, Yoji; Osaki, Tomohiro

2017-05-01

Blood analytes are easily used in routine clinical practice. Tumor markers (TMs) are useful in diagnosing, treating, and predicting prognosis of gastric cancer (GC). The prognostic nutritional index (PNI) was also recently found to be useful in predicting GC prognosis. The PNI and serum levels of CEA and CA19-9 of 453 patients with GC were measured to examine correlations between those levels and patients' prognoses. Of the 453 patients, 84 (18.5%) were positive for CEA and/or CA19-9 and therefore considered positive for TMs. Prognosis of patients who were TM+ was significantly worse than for those who were TM-. Mean PNI was 48.2 (range 27.7-63.6). ROC analysis indicated that 46.7 was the optimal PNI cutoff value. Prognosis of patients in the PNI Low group (<46.7) was significantly worse than in the PNI High group (≥46.7). Prognosis of patients who were both TM+ and PNI Low was significantly worse than that of patients who were either TM+ or PNI Low and those who were both TM- and PNI High . Multivariate analysis indicated that combination of TM and PNI was an independent prognostic indicator. The combination of TM and PNI offers accurate information about a patient's prognosis.

Magnetic ordering in TmGa.

PubMed

Cadogan, J M; Stewart, G A; Muñoz Pérez, S; Cobas, R; Hansen, B R; Avdeev, M; Hutchison, W D

2014-03-19

We have determined the magnetic structure of the intermetallic compound TmGa by high-resolution neutron powder diffraction and (169)Tm Mössbauer spectroscopy. This compound crystallizes in the orthorhombic (Cmcm) CrB-type structure and its magnetic structure is characterized by magnetic order of the Tm sublattice along the a-axis. The initial magnetic ordering occurs at 15(1) K and yields an incommensurate antiferromagnetic structure described by the propagation vector k1 = [0 0.275(2) 0]. At 12 K the dominant ferromagnetic ordering of the Tm sublattice along the a-axis develops in what appears to be a first-order transition. At 3 K the magnetic structure of TmGa is predominantly ferromagnetic but a weakened incommensurate component remains. The ferromagnetic Tm moment reaches 6.7(2) μB at 3 K and the amplitude of the remaining incommensurate component is 2.7(4) μB. The (169)Tm hyperfine magnetic field at 5 K is 631(1) T.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

PubMed Central

Kozubal, Mark A; Romine, Margaret; Jennings, Ryan deM; Jay, Zack J; Tringe, Susannah G; Rusch, Doug B; Beam, Jacob P; McCue, Lee Ann; Inskeep, William P

2013-01-01

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron-oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as ‘Geoarchaeota' or ‘novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today. PMID:23151644

37 CFR 102.34 - Specific exemptions.

Code of Federal Regulations, 2012 CFR

2012-07-01

.../DEPT-14; (D) Attorneys and Agents Registered to Practice Before the Office—COMMERCE/PAT-TM-1; (E... OF COMMERCE ADMINISTRATION DISCLOSURE OF GOVERNMENT INFORMATION Privacy Act § 102.34 Specific... are within this exemption are: COMMERCE/PAT-TM-6, COMMERCE/PAT-TM-7, COMMERCE/PAT-TM-8, COMMERCE/PAT...

37 CFR 102.34 - Specific exemptions.

Code of Federal Regulations, 2013 CFR

2013-07-01

.../DEPT-14; (D) Attorneys and Agents Registered to Practice Before the Office—COMMERCE/PAT-TM-1; (E... OF COMMERCE ADMINISTRATION DISCLOSURE OF GOVERNMENT INFORMATION Privacy Act § 102.34 Specific... are within this exemption are: COMMERCE/PAT-TM-6, COMMERCE/PAT-TM-7, COMMERCE/PAT-TM-8, COMMERCE/PAT...

Computational study of the heterodimerization between μ and δ receptors

NASA Astrophysics Data System (ADS)

Liu, Xin; Kai, Ming; Jin, Lian; Wang, Rui

2009-06-01

A growing body of evidence indicated that the G protein coupled receptors exist as homo- or hetero-dimers in the living cell. The heterodimerization between μ and δ opioid receptors has attracted researchers' particular interests, it is reported to display novel pharmacological and signalling regulation properties. In this study, we construct the full-length 3D-model of μ and δ opioid receptors using the homology modelling method. Threading program was used to predict the possible templates for the N- and C-terminus domains. Then, a 30 ns molecular dynamics simulations was performed with each receptor embedded in an explicit membrane-water environment to refine and explore the conformational space. Based on the structures extracted from the molecular dynamics, the likely interface of μ-δ heterodimer was investigated through the analysis of protein-protein docking, cluster, shape complementary and interaction energy. The computational modelling works revealed that the most likely interface of heterodimer was formed between the transmembrane1,7 (TM1,7) domains of μ receptor and the TM(4,5) domains of δ receptor, with emphasis on μ-TM1 and δ-TM4, the next likely interface was μ(TM6,7)-δ(TM4,5), with emphasis on μ-TM6 and δ-TM4. Our results were consistent with previous reports.

Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes.

PubMed

Taylor-Brown, Alyce; Bachmann, Nathan L; Borel, Nicole; Polkinghorne, Adam

2016-09-05

Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology. Using a metagenomics approach, the aim of this study was to characterise the genome of a novel chlamydial taxon from the choana of a captive snake. In doing so, we propose a new candidate species in the genus Chlamydia (Candidatus Chlamydia sanzinia) and reveal new information about the biological diversity of this important group of pathogens. We identified two chlamydial genomic contigs: a 1,113,073 bp contig, and a 7,504 bp contig, representing the chromosome and plasmid of Ca. Chlamydia sanzinia strain 2742-308, respectively. The 998 predicted coding regions include an expanded repertoire of outer membrane proteins (Pmps and Omps), some of which exhibited frameshift mutations, as well as several chlamydial virulence factors such as the translocating actin-recruitment phosphoprotein (Tarp) and macrophage inhibition potentiator (Mip). A suite of putative inclusion membrane proteins were also predicted. Notably, no evidence of a traditional chlamydial plasticity zone was identified. Phylogenetically, Ca. Chlamydia sanzinia forms a clade with C. pneumoniae and C. pecorum, distinct from former "Chlamydophila" species. Genomic characterisation of a novel uncultured chlamydiae from the first reptilian host has expanded our understanding of the diversity and biology of a genus that was thought to be the most well-characterised in this unique phylum. It is anticipated that this method will be suitable for characterisation of other novel chlamydiae.

LANDSAT-D investigations in snow hydrology

NASA Technical Reports Server (NTRS)

Dozier, J. (Principal Investigator)

1982-01-01

Snow reflectance in all 6 TM reflective bands, i.e., 1, 2, 3, 4, 5, and 7 was simulated using a delta-Eddington model. Snow reflectance in bands 4, 5, and 7 appear sensitive to grain size. It appears that the TM filters resemble a ""square-wave'' closely enough that a square-wave can be assumed in calculations. Integrated band reflectance over the actual response functions was calculated using sensor data supplied by Santa Barbara Research Center. Differences between integrating over the actual response functions and the equivalent square wave were negligible. Tables are given which show (1) sensor saturation radiance as a percentage of the solar constant, integrated through the band response function; (2) comparisons of integrations through the sensor response function with integrations over the equivalent square wave; and (3) calculations of integrated reflectance for snow over all reflective TM bands, and water and ice clouds with thickness of 1 mm water equivalent over TM bands 5 and 7. These calculations look encouraging for snow/cloud discrimination with TM bands 5 and 7.

Motion of the Tympanic Membrane after Cartilage Tympanoplasty Determined by Stroboscopic Holography

PubMed Central

Aarnisalo, Antti A.; Cheng, Jeffrey T.; Ravicz, Michael E.; Furlong, Cosme; Merchant, Saumil N.; Rosowski, John J.

2009-01-01

Stroboscopic holography was used to quantify dynamic deformations of the tympanic membrane (TM) of the entire surface of the TM before and after cartilage tympanoplasty of the posterior or posterior-superior part of the TM. Cartilage is widely used in tympanoplasties to provide mechanical stability for the TM. Three human cadaveric temporal bones were used. A 6 mm × 3 mm oval cartilage graft was placed through the widely opened facial recess onto the medial surface of the posterior or posterior-superior part of the TM. The graft was either in contact with the bony tympanic rim and manubrium or not. Graft thickness was either 0.5 or 1.0 mm. Stroboscopic holography produced displacement amplitude and phase maps of the TM surface in response to stimulus sound. Sound stimuli were 0.5, 1, 4 and 7 (or 8) kHz tones. Middle ear impedance was measured from the motion of the entire TM. Cartilage placement generally produced reductions in the motion of the TM apposed to the cartilage, especially at 4 kHz and 7 or 8 kHz. Some parts of the TM showed altered motion compared to the control in all three cases. In general, middle ear impedance was either unchanged or increased somewhat after cartilage reconstruction both at low (0.5 and 1 kHz) and high (4 and 7 kHz) frequencies. At 4 kHz, with the 1.0 mm thick graft that was in contact with the bony tympanic rim, the impedance slightly decreased. While our earlier work with time-averaged holography allowed us to observe differences in the pattern of TM motion caused by application of cartilage to the TM, stroboscopic holography is more sensitive to TM motions and allowed us to quantify the magnitude and phase of motion of each point on the TM surface. Nonetheless, our results are similar to those of our earlier work: The placement of cartilage on the medial surface of TM reduces the motion of the TM that apposes the cartilage. These obvious local changes occur even though the cartilage had little effect on the sound-induced motion of the stapes. PMID:19909803

Plasminogen Activator Inhibitor-1 Antagonist TM5484 Attenuates Demyelination and Axonal Degeneration in a Mice Model of Multiple Sclerosis.

PubMed

Pelisch, Nicolas; Dan, Takashi; Ichimura, Atsuhiko; Sekiguchi, Hiroki; Vaughan, Douglas E; van Ypersele de Strihou, Charles; Miyata, Toshio

2015-01-01

Multiple sclerosis (MS) is characterized by inflammatory demyelination and deposition of fibrinogen in the central nervous system (CNS). Elevated levels of a critical inhibitor of the mammalian fibrinolitic system, plasminogen activator inhibitor 1 (PAI-1) have been demonstrated in human and animal models of MS. In experimental studies that resemble neuroinflammatory disease, PAI-1 deficient mice display preserved neurological structure and function compared to wild type mice, suggesting a link between the fibrinolytic pathway and MS. We previously identified a series of PAI-1 inhibitors on the basis of the 3-dimensional structure of PAI-1 and on virtual screening. These compounds have been reported to provide a number of in vitro and in vivo benefits but none was tested in CNS disease models because of their limited capacity to penetrate the blood-brain barrier (BBB). The existing candidates were therefore optimized to obtain CNS-penetrant compounds. We performed an in vitro screening using a model of BBB and were able to identify a novel, low molecular PAI-1 inhibitor, TM5484, with the highest penetration ratio among all other candidates. Next, we tested the effects on inflammation and demyelination in an experimental allergic encephalomyelitis mice model. Results were compared to either fingolimod or 6α-methylprednisolone. Oral administration of TM5484 from the onset of signs, ameliorates paralysis, attenuated demyelination, and axonal degeneration in the spinal cord of mice. Furthermore, it modulated the expression of brain-derived neurotrophic factor, which plays a protective role in neurons against various pathological insults, and choline acetyltransferase, a marker of neuronal density. Taken together, these results demonstrate the potential benefits of a novel PAI-1 inhibitor, TM5484, in the treatment of MS.

Ligand binding to the human MT2 melatonin receptor: The role of residues in transmembrane domains 3, 6, and 7

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

Mazna, Petr; Berka, Karel; Jelinkova, Irena

To better understand the mechanism of interactions between G-protein-coupled melatonin receptors and their ligands, our previously reported homology model of human MT2 receptor with docked 2-iodomelatonin was further refined and used to select residues within TM3, TM6, and TM7 potentially important for receptor-ligand interactions. Selected residues were mutated and radioligand-binding assay was used to test the binding affinities of hMT2 receptors transiently expressed in HEK293 cells. Our data demonstrate that residues N268 and A275 in TM6 as well as residues V291 and L295 in TM7 are essential for 2-iodomelatonin binding to the hMT2 receptor, while TM3 residues M120, G121, V124,more » and I125 may participate in binding of other receptor agonists and/or antagonists. Presented data also hint at possible specific interaction between the side-chain of Y188 in second extracellular loop and N-acetyl group of 2-iodomelatonin.« less

Cubic sub-20 nm NaLuF(4)-based upconversion nanophosphors for high-contrast bioimaging in different animal species.

PubMed

Yang, Tianshe; Sun, Yun; Liu, Qian; Feng, Wei; Yang, Pengyuan; Li, Fuyou

2012-05-01

A new upconversion luminescence (UCL) nanophosphors based on host matrix of cubic NaLuF(4) with bright luminescence have been synthesized by a solvothermal method, facilitate the nanocrystals potential candidates for imaging in vivo, especially large-animals. The sub-20 nm NaLuF(4) co-doped Yb(3+) and Er(3+) (Tm(3+)) showed about 10-fold stronger UCL emission than that of corresponding hexagonal NaYF(4)-based nanocrystals with a 20 nm diameter. Near-infrared to near-infrared (NIR-to-NIR) UCL emission of PAA-coated NaLuF(4):20%Yb,1%Tm (PAA-Lu(Tm)) can penetrate >1.5 cm tissue of pork with high contrast. Based on super-strong UCL emission and deep penetration, PAA-Lu(Tm) as optical bioprobe has been demonstrated by in vivo UCL imaging of a normal black mouse, even rabbit with excellent signal-to-noise ratio. Furthermore, such cubic NaLuF(4)-based nanophosphor was applied in lymph node imaging of live Kunming mouse with rich white fur. Copyright © 2012 Elsevier Ltd. All rights reserved.

Response of some Thematic Mapper band ratios to variation in soil water content

NASA Technical Reports Server (NTRS)

Musick, H. Brad; Pelletier, Ramona E.

1986-01-01

Bidirectional reflectance to nadir in the reflective TM bands and the 1.15-1.3-micron band was measured in the laboratory as moisture content was varied in ten soils. Stronger absorption by water in TM5 and TM7 was expected to cause ratios of other bands to TM5 and TM7 to increase with water content, but in most cases these ratios were constant or decreased at low to intermediate water content and increased only at high moisture levels. Because these ratios were found to decrease as illumination elevation angle decreased, it was suggested that increased roughness resulting from the methods of moistening and mixing the soil may have tended to counteract the expected ratio increases.

Complete genome of the cellulolytic ruminal bacterium Ruminococcus albus 7

USDA-ARS?s Scientific Manuscript database

Ruminococcus albus 7 is a highly cellulolytic rumen bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome for this microbe. This genome will be useful for rumen microbiology, cellulosome biology, and in biofuel production, as one of its major fermentation product...

A Class of Visual Neurons with Wide-Field Properties Is Required for Local Motion Detection.

PubMed

Fisher, Yvette E; Leong, Jonathan C S; Sporar, Katja; Ketkar, Madhura D; Gohl, Daryl M; Clandinin, Thomas R; Silies, Marion

2015-12-21

Visual motion cues are used by many animals to guide navigation across a wide range of environments. Long-standing theoretical models have made predictions about the computations that compare light signals across space and time to detect motion. Using connectomic and physiological approaches, candidate circuits that can implement various algorithmic steps have been proposed in the Drosophila visual system. These pathways connect photoreceptors, via interneurons in the lamina and the medulla, to direction-selective cells in the lobula and lobula plate. However, the functional architecture of these circuits remains incompletely understood. Here, we use a forward genetic approach to identify the medulla neuron Tm9 as critical for motion-evoked behavioral responses. Using in vivo calcium imaging combined with genetic silencing, we place Tm9 within motion-detecting circuitry. Tm9 receives functional inputs from the lamina neurons L3 and, unexpectedly, L1 and passes information onto the direction-selective T5 neuron. Whereas the morphology of Tm9 suggested that this cell would inform circuits about local points in space, we found that the Tm9 spatial receptive field is large. Thus, this circuit informs elementary motion detectors about a wide region of the visual scene. In addition, Tm9 exhibits sustained responses that provide a tonic signal about incoming light patterns. Silencing Tm9 dramatically reduces the response amplitude of T5 neurons under a broad range of different motion conditions. Thus, our data demonstrate that sustained and wide-field signals are essential for elementary motion processing. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography

PubMed Central

Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C.; Gulsen, Gultekin

2016-01-01

Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed “temperature-modulated fluorescence tomography” (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40 mm × W :100 mm) is recovered as an elongated object in the conventional FT (x = 4.5 mm; y = 10.4 mm), while TM-FT recovers it successfully in both directions (x = 3.8 mm; y = 4.6 mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT. PMID:26368884

Optical decoherence studies of Tm3 +:Y3Ga5O12

NASA Astrophysics Data System (ADS)

Thiel, C. W.; Sinclair, N.; Tittel, W.; Cone, R. L.

2014-12-01

Decoherence of the 795 nm 3H6 to 3H4 transition in 1 %Tm3 +:Y3Ga5O12 (Tm:YGG) is studied at temperatures as low as 1.2 K. The temperature, magnetic field, frequency, and time scale (spectral diffusion) dependence of the optical coherence lifetime is measured. Our results show that the coherence lifetime is impacted less by spectral diffusion than other known thulium-doped materials. Photon echo excitation and spectral hole burning methods reveal uniform decoherence properties and the possibility to produce full transparency for persistent spectral holes across the entire 56 GHz inhomogeneous bandwidth of the optical transition. Temperature-dependent decoherence is well described by elastic Raman scattering of phonons with an additional weaker component that may arise from a low density of glass-like dynamic disorder modes (two-level systems). Analysis of the observed behavior suggests that an optical coherence lifetime approaching 1 ms may be possible in this system at temperatures below 1 K for crystals grown with optimized properties. Overall, we find that Tm:YGG has superior decoherence properties compared to other Tm-doped crystals and is a promising candidate for applications that rely on long coherence lifetimes, such as optical quantum memories and photonic signal processing.

Ecology of the oral microbiome: beyond bacteria

PubMed Central

Baker, Jonathon L.; Bor, Batbileg; Agnello, Melissa; Shi, Wenyuan; He, Xuesong

2017-01-01

Although great strides have been made in understanding the complex bacterial community inhabiting the human oral cavity, for a variety of (mainly technical) reasons the ecological contributions of oral fungi, viruses, phages, and the candidate phyla radiation (CPR) group of ultra-small bacteria have remained understudied. Several recent reports have illustrated the diversity and importance of these organisms in the oral cavity, while TM7x and Candida albicans have served as crucial paradigms for CPR species and oral fungi, respectively. A comprehensive understanding of the oral microbiota and its influence on host health and disease will require a holistic view that emphasizes interactions among different residents within the oral community, as well as their interaction with the host. PMID:28089325

Angiopoietin-like 7 Secretion Is Induced by Glaucoma Stimuli and Its Concentration Is Elevated in Glaucomatous Aqueous Humor

PubMed Central

Kuchtey, John; Källberg, Maria E.; Gelatt, Kirk N.; Rinkoski, Tommy; Komàromy, András M.; Kuchtey, Rachel W.

2010-01-01

Purpose To investigate the possibility that Angiopoietin-like 7 (ANGPTL7) protein is involved in the pathogenesis of glaucoma. Methods Primary human trabecular meshwork (TM) cells and corneoscleral explants were stimulated with either dexamethasone (DEX) or transforming growth factor β (TGFβ), and ANGPTL7 protein secreted into culture medium was determined by Western blot analysis. The effect of stable overexpression of ANGPTL7 in transfected immortalized TM cell lines on collagen expression was investigated by immunocytochemistry. Localization of ANGPTL7 protein in human eyes was determined by immunohistochemistry. The concentration of ANGPTL7 protein in aqueous humor (AH) from patients with glaucoma and control patients was compared by Western blot analysis. The beagle model of primary open-angle glaucoma (POAG) was used to correlate ANGPTL7 protein levels in canine AH with disease progression. Results TGFβ and DEX stimulated secretion of ANGPTL7 protein by TM cells and corneoscleral explants. Overexpression of ANGPTL7 by immortalized TM cell lines increased expression of type I collagen. Expression of ANGPTL7 protein was located in the corneal stroma, near the limbus, and throughout the sclera, with lower expression in the TM. In the lamina cribrosa, ANGPTL7 expression was associated with the cribriform plates. The concentration of ANGPTL7 protein was elevated in AH from patients with glaucoma and increased as disease progressed in POAG beagle dogs. Conclusions Induction of ANGPTL7 secretion by glaucoma stimuli and increased concentration of ANGPTL7 in glaucomatous AH suggest that ANGPTL7 is overexpressed in glaucoma. Since overexpression of ANGPTL7 increases collagen expression, a potential disease mechanism, ANGPTL7 could have a pathogenic role in glaucoma, and may serve as a potential therapeutic target. PMID:18421092

Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10

PubMed Central

Tanaka, Yasuhiro; Tamaki, Hideyuki; Matsuzawa, Hiroaki; Nigaya, Masahiro; Mori, Kazuhiro; Kamagata, Yoichi

2012-01-01

A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40–4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5–3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms. PMID:22791047

Engineering of a Novel Saccharomyces cerevisiae Wine Strain with a Respiratory Phenotype at High External Glucose Concentrations

PubMed Central

Henricsson, C.; de Jesus Ferreira, M. C.; Hedfalk, K.; Elbing, K.; Larsson, C.; Bill, R. M.; Norbeck, J.; Hohmann, S.; Gustafsson, L.

2005-01-01

The recently described respiratory strain Saccharomyces cerevisiae KOY.TM6*P is, to our knowledge, the only reported strain of S. cerevisiae which completely redirects the flux of glucose from ethanol fermentation to respiration, even at high external glucose concentrations (27). In the KOY.TM6*P strain, portions of the genes encoding the predominant hexose transporter proteins, Hxt1 and Hxt7, were fused within the regions encoding transmembrane (TM) domain 6. The resulting chimeric gene, TM6*, encoded a chimera composed of the amino-terminal half of Hxt1 and the carboxy-terminal half of Hxt7. It was subsequently integrated into the genome of an hxt null strain. In this study, we have demonstrated the transferability of this respiratory phenotype to the V5 hxt1-7Δ strain, a derivative of a strain used in enology. We also show by using this mutant that it is not necessary to transform a complete hxt null strain with the TM6* construct to obtain a non-ethanol-producing phenotype. The resulting V5.TM6*P strain, obtained by transformation of the V5 hxt1-7Δ strain with the TM6* chimeric gene, produced only minor amounts of ethanol when cultured on external glucose concentrations as high as 5%. Despite the fact that glucose flux was reduced to 30% in the V5.TM6*P strain compared with that of its parental strain, the V5.TM6*P strain produced biomass at a specific rate as high as 85% that of the V5 wild-type strain. Even more relevant for the potential use of such a strain for the production of heterologous proteins and also of low-alcohol beverages is the observation that the biomass yield increased 50% with the mutant compared to its parental strain. PMID:16204537

Engineering of a novel Saccharomyces cerevisiae wine strain with a respiratory phenotype at high external glucose concentrations.

PubMed

Henricsson, C; de Jesus Ferreira, M C; Hedfalk, K; Elbing, K; Larsson, C; Bill, R M; Norbeck, J; Hohmann, S; Gustafsson, L

2005-10-01

The recently described respiratory strain Saccharomyces cerevisiae KOY.TM6*P is, to our knowledge, the only reported strain of S. cerevisiae which completely redirects the flux of glucose from ethanol fermentation to respiration, even at high external glucose concentrations (27). In the KOY.TM6*P strain, portions of the genes encoding the predominant hexose transporter proteins, Hxt1 and Hxt7, were fused within the regions encoding transmembrane (TM) domain 6. The resulting chimeric gene, TM6*, encoded a chimera composed of the amino-terminal half of Hxt1 and the carboxy-terminal half of Hxt7. It was subsequently integrated into the genome of an hxt null strain. In this study, we have demonstrated the transferability of this respiratory phenotype to the V5 hxt1-7Delta strain, a derivative of a strain used in enology. We also show by using this mutant that it is not necessary to transform a complete hxt null strain with the TM6* construct to obtain a non-ethanol-producing phenotype. The resulting V5.TM6*P strain, obtained by transformation of the V5 hxt1-7Delta strain with the TM6* chimeric gene, produced only minor amounts of ethanol when cultured on external glucose concentrations as high as 5%. Despite the fact that glucose flux was reduced to 30% in the V5.TM6*P strain compared with that of its parental strain, the V5.TM6*P strain produced biomass at a specific rate as high as 85% that of the V5 wild-type strain. Even more relevant for the potential use of such a strain for the production of heterologous proteins and also of low-alcohol beverages is the observation that the biomass yield increased 50% with the mutant compared to its parental strain.

Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum

PubMed Central

Griffiths, Emma; Gupta, Radhey S.

2004-01-01

The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase β′ subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (σ70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., σ70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group. PMID:15126471

Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization.

PubMed

Smaldone, Giovanni; Berisio, Rita; Balasco, Nicole; D'Auria, Sabato; Vitagliano, Luigi; Ruggiero, Alessia

2018-05-31

Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP 20-233 ) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP 20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP 20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP 20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography.

PubMed

Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C; Gulsen, Gultekin

2015-09-01

Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed "temperature-modulated fluorescence tomography" (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40  mm×W:100  mm) is recovered as an elongated object in the conventional FT (x=4.5  mm; y=10.4  mm), while TM-FT recovers it successfully in both directions (x=3.8  mm; y=4.6  mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT.

LANDSAT-D investigations in snow hydrology

NASA Technical Reports Server (NTRS)

Dozier, J. (Principal Investigator)

1982-01-01

The sample LANDSAT-4 TM tape (7 bands) of NE Arkansas/Tennessee area was received and displayed. Snow reflectance in all 6 TM reflective bands, i.e. 1, 2, 3, 4, 5, and 7 was simulated, using Wiscombe and Warren's (1980) delta-Eddington model. Snow reflectance in bands 4, 5, and 7 appear sensitive to grain size. One of the objectives is to interpret surface optical grain size of snow, for spectral extension of albedo. While TM data of the study area are not received, simulation results are encouraging. It also appears that the TM filters resemble a "square-wave" closely enough to permit assuming a square-wave in calculations. Integrated band reflectance over the actual response functions was simulated, using sensor data supplied by Santa Barbara Research Center. Differences between integrating over the actual response functions and the equivalent square wave were negligible.

Long-Term Follow-Up of Testicular Microlithiasis in Children and Adolescents: Multicenter Prospective Cohort Study of the Italian Society of Pediatric Urology.

PubMed

Marte, Antonio; Pintozzi, Lucia; Cretì, Giuseppe; Chiesa, Pierluigi Lelli; Renzo, Dacia Di; Gasparella, Marco; Maggio, Giovanni Di; Bagnara, Vincenzo; Merlini, Emilio; Tadini, Barbara; Caldarulo, Eustachio; Sangiorgio, Luciano; Battaglino, Gianfranco; Nappo, Simona Gerocarni; Caione, Paolo

2017-04-01

Introduction  Testicular microlithiasis (TM), characterized by the presence of intratubular calcifications in a single or both the gonads, is an uncommon entity with unknown etiology and outcome in pediatric and adolescent age. In this study, the results of a multicenter long-term survey are presented. Materials and Methods  From 11 units of pediatric urology/surgery, patients with TM were identified and yearly, followed up in a 7-year period, adopting a specific database. The recorded items were: age at diagnosis, presenting symptoms/associated abnormalities, ultrasonographic finding, surgery and histology at biopsy, if performed. Results  Out of 85 patients, 81 were evaluated yearly (4 patients lost to follow-up). TM was bilateral in 66.6% of the patients. Associate genital abnormalities were present in 90%, more frequently undescended/retractile testis (23.4%) and varicocele (22.2%). TM remained unchanged at 4.7 years follow-up in 77 patients (93.8%) and was reduced in 4 patients after 1 to 5 years of inguinoscrotal surgery. Orchiectomy was performed in three patients (3.7%), one for severe testicular hypoplasia and two for seminoma (2.5%), respectively, concurrent and metachronous to diagnosis of TM. Tumorectomy with parenchymal sparing surgery was performed in a teratoma associated with TM. Conclusion  TM is a controversial entity, often associated with several inguinogenital features, which rarely can recover. Testicular malignancy, although present in TM, has not proven definitively associated to microliths. Proper counseling, yearly ultrasound, and self-examination are long-term recommended. Georg Thieme Verlag KG Stuttgart · New York.

Papain cleavage of the 38,000-dalton fragment inhibits the binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate to lys-539 on the 60,000-dalton fragment in human band 3.

PubMed

Yamaguchi, Takeo; Kojima, Hideaki; Kawaguchi, Shiori; Shimada, Maiko; Aso, Haruka

2017-08-01

Human band 3 is a 98-kDa transmembrane (TM) protein comprising 14 TM segments. Papain cleavages band 3 into 38- and 60-kDa fragments. Under vigorous conditions, the cleavage of the loop region between the TM 7 of gate domain and the TM 8 of core domain in the 38-kDa fragment produces 7- and 31-kDa fragments. Conformational changes of the TM 5 segment containing Lys-539 by cleavage of the 38-kDa fragment remain unclear. Pressure-induced haemolysis of erythrocytes was suppressed by binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate (DIDS) to Lys-539. Such effect of DIDS was not observed upon cleavage of the 38-kDa fragment, because of inhibition of DIDS binding to Lys-539. Using fluorescence of DIDS labelled to Lys-539, conformational changes of band 3 were examined. Fluorescence spectra demonstrated that the molecular motion of DIDS is more restricted upon digestion of the 38-kDa fragment. Interestingly, the quenching of DIDS fluorescence showed that Hg2+ is less accessible to DIDS upon digestion of the 38-kDa fragment. Taken together, we propose that the conformational changes of the TM 5 segment characterized by the sequestration and restricted motion of Lys-539 are induced by the cleavage of the loop region between the TM 7 and the TM 8. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm.

PubMed

Oliveira, R R D S; Fermiano, D; Feres, M; Figueiredo, L C; Teles, F R F; Soares, G M S; Faveri, M

2016-06-01

In recent years, several new periodontal taxa have been associated with the etiology of periodontitis. A recent systematic review provides further support for the pathogenic role of 17 species/phylotypes. Thus, the aim of this study was to assess the prevalence and levels of these species in subjects with generalized chronic periodontitis (GChP; n = 30), generalized aggressive periodontitis (GAgP; n = 30), and periodontal health (PH; n = 30). All subjects underwent clinical and microbiological assessment. Nine subgingival plaque samples were collected from each subject and analyzed for their content of 20 bacterial species/phylotypes through the RNA-oligonucleotide quantification technique. Subjects from the GChP and GAgP groups presented the highest mean values for all clinical parameters in comparison with the PH group (P < 0.05). Subjects with GChP and GAgP showed significantly higher mean levels of Bacteroidetes sp. human oral taxon (HOT) 274, Fretibacterium sp. HOT 360, and TM7 sp. HOT 356 phylotypes, as well as higher mean levels of Filifactor alocis, Fretibacterium fastidiosum, Porphyromonas gingivalis, Tannerella forsythia, and Selenomonas sputigena species than PH subjects (P < 0.05). GAgP subjects presented higher mean levels of TM7 sp. HOT 356 and F. alocis than GChP subjects (P < 0.05). A significantly higher mean prevalence of Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, and Fretibacterium sp. HOT 362 was found in subjects with GChP and GAgP than in PH subjects. Mean levels of P. gingivalis (r = 0.68), T. forsythia (r = 0.62), F. alocis (r = 0.51, P = 0.001), and Fretibacterium sp. HOT 360 (r = 0.41) were correlated with pocket depth (P < 0.001). In conclusion, Bacteroidales sp. HOT 274, Desulfobulbus sp. HOT 041, Fretibacterium sp. HOT 360, Fretibacterium sp. HOT 362, and TM7 sp. HOT 356 phylotypes, in addition to F. alocis, F. fastidiosum, and S. sputigena, seem to be associated with periodontitis, and their role in periodontal pathogenesis should be further investigated. © International & American Associations for Dental Research 2016.

Diode pumped tunable lasers based on Tm:CaF2 and Tm:Ho:CaF2 ceramics

NASA Astrophysics Data System (ADS)

Šulc, Jan; Němec, Michal; Jelinková, Helena; Doroshenko, Maxim E.; Fedorov, Pavel P.; Osiko, Vyacheslav V.

2014-02-01

The Tm:CaF2 (4% of TmF3) and Tm:Ho:CaF2 (2% of TmF3, 0.3% of HoF3) ceramics, prepared using hot pressing, and hot formation technique had been used as an active medium of diode pumped mid-infrared tunable laser. A fibre (core diameter 400 μm, NA = 0.22) coupled laser diode (LIMO, HLU30F400-790) was used to longitudinal pumping. The laser diode was operating in the pulsed regime (6 ms pulse length, 10 Hz repetition rate). The duty-cycle 6% ensures a low thermal load even under the maximum diode pumping power amplitude 25W (ceramics samples were only air-cooled). The laser diode emission wavelength was 786 nm. The 80mm long semi-hemispherical laser resonator consisted of a flat pumping mirror (HR @ 1.85 - 2.15 μm, HT @ 0.78 μm) and a curved (r = 150mm) output coupler with a reflectivity of ˜ 98% @ 1.85 - 2.0 μm for Tm:CaF2 laser or ˜ 99.5% @ 2.0 - 2.15 μm for Ho:Tm:CaF2. Tuning of the laser was accomplished by using a birefringent filter (single 1.5mm thick quartz plate) placed inside the optical resonator at the Brewster angle. Both samples offered broad and smooth tuning possibilities in mid-IR spectral range and the lasers were continuously tunable over ˜ 100 nm. The obtained Tm:CaF2 tunability ranged from 1892 to 1992nm (the maximum output energy 1.8mJ was reached at 1952nm for absorbed pumping energy 78 mJ). In case of Tm:Ho:CaF2 laser tunability from 2016 to 2111nm was reached (the maximum output energy 1.5mJ was reached at 2083nm for absorbed pumping energy 53 mJ). Both these material are good candidates for a future investigation of high energy, ultra-short, laser pulse generation.

Tm-doped TiO2 and Tm2Ti2O7 pyrochlore nanoparticles: enhancing the photocatalytic activity of rutile with a pyrochlore phase.

PubMed

De Los Santos, Desiré M; Navas, Javier; Aguilar, Teresa; Sánchez-Coronilla, Antonio; Fernández-Lorenzo, Concha; Alcántara, Rodrigo; Piñero, Jose Carlos; Blanco, Ginesa; Martín-Calleja, Joaquín

2015-01-01

Tm-doped TiO2 nanoparticles were synthesized using a water-controlled hydrolysis reaction. Analysis was performed in order to determine the influence of the dopant concentration and annealing temperature on the phase, crystallinity, and electronic and optical properties of the resulting material. Various characterization techniques were utilized such as X-ray diffraction, Raman spectroscopy, X-ray photoelectron spectroscopy and UV-vis spectroscopy. For the samples annealed at 773 and 973 K, anatase phase TiO2 was obtained, predominantly internally doped with Tm(3+). ICP-AES showed that a doping concentration of up to 5.8 atom % was obtained without reducing the crystallinity of the samples. The presence of Tm(3+) was confirmed by X-ray photoelectron spectroscopy and UV-vis spectroscopy: the incorporation of Tm(3+) was confirmed by the generation of new absorption bands that could be assigned to Tm(3+) transitions. Furthermore, when the samples were annealed at 1173 K, a pyrochlore phase (Tm2Ti2O7) mixed with TiO2 was obtained with a predominant rutile phase. The photodegradation of methylene blue showed that this pyrochlore phase enhanced the photocatalytic activity of the rutile phase.

Hypolipidemic activity of Taraxacum mongolicum associated with the activation of AMP-activated protein kinase in human HepG2 cells.

PubMed

Liu, Yan-Jin; Shieh, Po-Chuen; Lee, Jang-Chang; Chen, Fu-An; Lee, Chih-Hung; Kuo, Sheng-Chu; Ho, Chi-Tang; Kuo, Daih-Huang; Huang, Li-Jiau; Way, Tzong-Der

2014-08-01

This study investigated the hypolipidemic effect and potential mechanisms of T. mongolicum extracts. T. mongolicum was extracted by refluxing three times with water (TM-1), 50% ethanol (TM-2) and 95% ethanol (TM-3). TM-2 contained components with the most effective hypolipidemic potentials in HepG2 cells. Extended administration of TM-2 stimulated a significant reduction in body weight and levels of serum triglyceride LDL-C and total cholesterol in rats. To evaluate the bioactive compounds, we successively fractionated TM-2 with n-hexane (TM-4), dichloromethane (TM-5), ethyl acetate (TM-6), and water (TM-7). TM-4 fraction had the most effective hypolipidemic potential in HepG2 cells, and it decreased the expression of fatty acid synthase (FASN) and inhibited the activity of acetyl-coenzyme A carboxylase (ACC) through the phosphorylation of AMP-activated protein kinase (AMPK). Linoleic acid, phytol and tetracosanol are bioactive compounds identified from TM-4. These results suggest that T. mongolicum is expected to be useful for hypolipidemic effects.

High Energy Directly Pumped Ho:YLF Laser

NASA Technical Reports Server (NTRS)

Petros, Mulugeta; Yu, Ji-Rong; Singh, Upendra N.; Barnes, Norman P.

2000-01-01

The most commonly used crystal architecture to produce 2 micrometer laser is co-doping Ho and Tm into a single host crystal. In this method, the stored energy transfer from the Tm (3)F4 to the Ho (5)I7 manifold is not fast enough to warrant high efficiency for short pulse applications. By separating the Ho and the Tm ions and doping the Tm in YALO3 and the Ho in YLF, we were able to directly pump the Ho (5)I7 manifold with 1.94 micrometers. The Ho:YLF laser has produced 33 mJ at 2.062 micrometers with a quantum efficiency of 0.88. The performance of each laser will be presented.

Raman microscopy of lithium-manganese-rich transition metal oxide cathodes

DOE PAGES

Ruther, Rose E.; Callender, Andrew F.; Zhou, Hui; ...

2014-11-15

Lithium-rich and manganese-rich (LMR) layered transition metal (TM) oxide composites with general formula xLi 2MnO 3·(1-x)LiMO 2 (M = Ni, Co, Mn) are promising cathode candidates for high energy density lithium ion batteries. Lithium-manganese-rich TM oxides crystallize as a nanocomposite layered phase whose structure further evolves with electrochemical cycling. Raman spectroscopy is a powerful tool to monitor the crystal chemistry and correlate phase changes with electrochemical behavior. While several groups have reported Raman spectra of lithium rich TM oxides, the data show considerable variability in terms of both the vibrational features observed and their interpretation. In this paper, Raman microscopymore » is used to investigate lithium-rich and manganese-rich TM cathodes as a function of voltage and electrochemical cycling at various temperatures. No growth of a spinel phase is observed within the cycling conditions. However, analysis of the Raman spectra does indicate the structure of LMR-NMC deviates significantly from an ideal layered phase. Finally, the results also highlight the importance of using low laser power and large sample sizes to obtain consistent data sets.« less

Telemedicine in wound care: a review.

PubMed

Chanussot-Deprez, Caroline; Contreras-Ruiz, José

2013-02-01

Telemedicine (TM) is a new, rapidly evolving area and can be of great value in the provision of healthcare to remote and rural populations. Wound healing and wound management are prime candidates for TM. The treatment of skin ulcers requires frequent assessments of local wound status and adjustment of therapy. The availability of reasonably priced photographic equipment and quick electronic transfer of high-quality digital images should make the assessment of wound status by remote experts possible. Several studies showing the feasibility and the usefulness of teleconsultations in dermatology have already been described in the literature, and high accordance for diagnosis and treatment between face-to-face visits and teleconsultations has been reported. Some used digital photographs and sent the image and clinical data via the Internet to a wound care specialist (store and forward), whereas others used a webcam (televideoconferencing). Tele-wound care offers great potential for the future in chronic wound care. By reducing the need to travel long distances to the hospital or to consult with a physician, TM decreases the costs and improves the quality of life for patients with chronic wounds, while still maintaining high standards of wound care. The intent of TM is to reduce, in a clinically equivalent way, the number of visits to a specialized clinic, but not necessarily to eliminate all visits. Further well-designed research is necessary to understand how best to deploy TM services in healthcare.

Sensitivity-enhanced Tm3+/Yb3+ co-doped YAG single crystal optical fiber thermometry based on upconversion emissions

NASA Astrophysics Data System (ADS)

Yu, Lu; Ye, Linhua; Bao, Renjie; Zhang, Xianwei; Wang, Li-Gang

2018-03-01

Optical thermometry based on Y3Al5O12 (YAG) single crystal optical fiber with end Tm3+/Yb3+ co-doped is presented. The YAG crystal fiber with end Tm3+/Yb3+ co-doped was grown by laser heated pedestal growth (LHPG) method. Under a 976 nm laser diode excitation, the upconversion (UC) emissions, originating from 3F2,3 →3H6 and 3H4 →3H6 transitions of Tm3+ ions, were investigated in the temperature range from 333 K to 733 K. Interestingly, the UC emission intensity of 3F2,3 →3H6 transition was significantly enhanced with increase of temperature, as compared with the other Tm3+/Yb3+ co-doped materials. The temperature dependence of fluorescence intensity ratio (FIR) of these two emission bands (3F2,3/3H4 →3H6) suggests that this doped YAG crystal fiber can be used as a highly sensitive optical thermal probe, which demonstrates a high absolute sensitivity with the maximum value of 0.021 K-1 at 733 K. In addition, due to the compact structure, strong mechanical strength and high thermal stability, such thermal probe may be a more promising candidate for temperature sensor with a high spatial resolution.

A definitive calibration record for the Landsat-5 thematic mapper anchored to the Landsat-7 radiometric scale

USGS Publications Warehouse

Teillet, P.M.; Helder, D.L.; Ruggles, T.A.; Landry, R.; Ahern, F.J.; Higgs, N.J.; Barsi, J.; Chander, G.; Markham, B.L.; Barker, J.L.; Thome, K.J.; Schott, J.R.; Palluconi, Frank Don

2004-01-01

A coordinated effort on the part of several agencies has led to the specification of a definitive radiometric calibration record for the Landsat-5 thematic mapper (TM) for its lifetime since launch in 1984. The time-dependent calibration record for Landsat-5 TM has been placed on the same radiometric scale as the Landsat-7 enhanced thematic mapper plus (ETM+). It has been implemented in the National Landsat Archive Production Systems (NLAPS) in use in North America. This paper documents the results of this collaborative effort and the specifications for the related calibration processing algorithms. The specifications include (i) anchoring of the Landsat-5 TM calibration record to the Landsat-7 ETM+ absolute radiometric calibration, (ii) new time-dependent calibration processing equations and procedures applicable to raw Landsat-5 TM data, and (iii) algorithms for recalibration computations applicable to some of the existing processed datasets in the North American context. The cross-calibration between Landsat-5 TM and Landsat-7 ETM+ was achieved using image pairs from the tandem-orbit configuration period that was programmed early in the Laridsat-7 mission. The time-dependent calibration for Landsat-5 TM is based on a detailed trend analysis of data from the on-board internal calibrator. The new lifetime radiometric calibration record for Landsat-5 will overcome problems with earlier product generation owing to inadequate maintenance and documentation of the calibration over time and will facilitate the quantitative examination of a continuous, near-global dataset at 30-m scale that spans almost two decades.

Conformational states of the full-length glucagon receptor

PubMed Central

Yang, Linlin; Yang, Dehua; de Graaf, Chris; Moeller, Arne; West, Graham M.; Dharmarajan, Venkatasubramanian; Wang, Chong; Siu, Fai Y.; Song, Gaojie; Reedtz-Runge, Steffen; Pascal, Bruce D.; Wu, Beili; Potter, Clinton S.; Zhou, Hu; Griffin, Patrick R.; Carragher, Bridget; Yang, Huaiyu; Wang, Ming-Wei; Stevens, Raymond C.; Jiang, Hualiang

2015-01-01

Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biology approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Molecular dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation associated with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism. PMID:26227798

Benthic Community Response to Hypoxia: Baseline Data

DTIC Science & Technology

2009-01-01

were represented by six different phyla, namely Annelida, Sipuncula, Arthropoda, Cnidaria , Mollusca and Echinodermata (Table II). The phylum Annelida...was solely represented by polychaetes and the phylum Cnidaria was represented solely by hydroids. However, the phylum Mollusca was represented by

Telemedical support to improve glycemic control in adolescents with type 1 diabetes mellitus.

PubMed

Rami, Birgit; Popow, Christian; Horn, Werner; Waldhoer, Thomas; Schober, Edith

2006-10-01

In this paper, we evaluated the feasibility of a telemedical (TM) support program and its effect on glycemic control in adolescents with type 1 diabetes mellitus (T1DM). Thirty-six adolescents (m=20, median age at the start of the study: 15.3 years (range: 10.7-19.3 years), median age at diagnosis: 9.3 years (2.1-13.8 years), median duration of disease: 6.4 years (1.0-12.8 years), HbA1c>8%, all on intensified insulin therapy) were randomized in a crossover trial over 6 months (3 months with TM, 3 months with conventional support and paper diary (PD)). During the TM phase, the patients sent their data (date, time, blood glucose, carbohydrate intake, insulin dosage) via mobile phone, at least daily, to our server and diabetologists sent back their advice via short message service (SMS) once a week. Glycemic control improved during the TM phase, while it deteriorated during the PD phase: TM-PD group HbA1c (%, median (range)): 9.05 (8-11.3) (at 0 months), 8.9 (6.9-11.3) (at 3 months), and 9.2 (7.4-12.6) (at 6 months), and PD-TM group: 8.9 (8.3-11.6), 9.9 (8.1-11), and 8.85 (7.3-11.7) (p<0.05). Patients rated the TM support program to be a good idea. Technical problems with General Packet Radio Service (GPRS) data transmission led to data loss and decreased patient satisfaction. Our telemedical support program, VIE-DIAB, proved to be feasible in adolescents and helped to improve glycemic control.

AN ANGIOTENSIN II TYPE 1 RECEPTOR ACTIVATION SWITCH PATCH REVEALED THROUGH EVOLUTIONARY TRACE ANALYSIS

PubMed Central

Bonde, Marie Mi; Yao, Rong; Ma, Jian-Nong; Madabushi, Srinivasan; Haunsø, Stig; Burstein, Ethan S.; Whistler, Jennifer L.; Sheikh, Søren P.; Lichtarge, Olivier; Hansen, Jakob Lerche

2010-01-01

Seven transmembrane (7TM) or G protein-coupled receptors constitute a large superfamily of cell surface receptors sharing a structural motif of seven transmembrane spanning alpha helices. Their activation mechanism most likely involves concerted movements of the transmembrane helices, but remains to be completely resolved. Evolutionary Trace (ET) analysis is a computational method, which identifies clusters of functionally important residues by integrating information on evolutionary important residue variations with receptor structure. Combined with known mutational data, ET predicted a patch of residues in the cytoplasmic parts of TM2, TM3, and TM6 to form an activation switch that is common to all family A 7TM receptors. We tested this hypothesis in the rat Angiotensin II (Ang II) type 1 (AT1) receptor. The receptor has important roles in the cardiovascular system, but has also frequently been applied as a model for 7TM receptor activation and signaling. Six mutations: F66A, L67R, L70R, L119R, D125A, and I245F were targeted to the putative switch and assayed for changes in activation state by their ligand binding, signaling, and trafficking properties. All but one receptor mutant (that was not expressed well) displayed phenotypes associated with changed activation state, such as increased agonist affinity or basal activity, promiscuous activation, or constitutive internalization highlighting the importance of testing different signaling pathways. We conclude that this evolutionary important patch mediates interactions important for maintaining the inactive state. More broadly, these observations in the AT1 receptor are consistent with computational predictions of a generic role for this patch in 7TM receptor activation. PMID:20227396

Inhibition of Lung Cancer Growth in Mice by Dietary Mixed Tocopherols

PubMed Central

Lambert, Joshua D.; Lu, Gang; Lee, Mao-Jung; Hu, Jennifer; Ju, Jihyeung; Yang, Chung S.

2009-01-01

Tocopherols are lipophilic antioxidants found in vegetable oils. Here, we examined the growth inhibitory effect of a γ-tocopherol-enriched tocopherol mixture (γTmT) against CL13 murine lung cancer cells grown in culture and as subcutaneous tumors in A/J mice. We found γTmT had no effect after 2 d and weakly inhibited the growth of CL13 in culture after 5 d (28% growth inhibition at 80 µM). Dietary treatment with 0.1% and 0.3% γTmT for 50 d inhibited the growth of CL13 tumors in A/J mice by 53.9 and 80.5%, respectively. Histopathological analysis revealed an increase in tumor necrosis compared to control tumors (80% and 240% increase by 0.1% and 0.3% γTmT, respectively). Dietary treatment with γTmT dose-dependently increased γ- (10.0 – 37.6-fold) and δ-tocopherol (8.9 – 26.7-fold) in the tumors of treated mice compared to controls. Dietary treatment with γTmT also increased plasma γ- (5.4 – 6.7-fold) and δ-tocopherol (5.5 – 7-fold). Whereas others have demonstrated the cancer preventive activity of γTmT against mammary and colon cancer, this is the first report of growth inhibitory activity against lung cancer. Further studies are needed to determine the underlying mechanisms for this anticancer activity, and to determine if such activity occurs in other models of cancer. PMID:19557822

The rat ErbB2 tyrosine kinase receptor produced in plants is immunogenic in mice and confers protective immunity against ErbB2(+) mammary cancer.

PubMed

Matić, Slavica; Quaglino, Elena; Arata, Lucia; Riccardo, Federica; Pegoraro, Mattia; Vallino, Marta; Cavallo, Federica; Noris, Emanuela

2016-01-01

The rat ErbB2 (rErbB2) protein is a 185-kDa glycoprotein belonging to the epidermal growth factor-related proteins (ErbB) of receptor tyrosine kinases. Overexpression and mutations of ErbB proteins lead to several malignancies including breast, lung, pancreatic, bladder and ovary carcinomas. ErbB2 is immunogenic and is an ideal candidate for cancer immunotherapy. We investigated the possibility of expressing the extracellular (EC) domain of rErbB2 (653 amino acids, aa) in Nicotiana benthamiana plants, testing the influence of the 23 aa transmembrane (TM) sequence on protein accumulation. Synthetic variants of the rErbB2 gene portion encoding the EC domain, optimized with a human codon usage and either linked to the full TM domain (rErbB2_TM, 676 aa), to a portion of it (rErbB2-pTM, 662 aa), or deprived of it (rErbB2_noTM, 653 aa) were cloned in the pEAQ-HT expression vector as 6X His tag fusions. All rErbB2 variants (72-74.5 kDa) were transiently expressed, but the TM was detrimental for rErbB2 EC accumulation. rERbB2_noTM was the most expressed protein; it was solubilized and purified with Nickel affinity resin. When crude soluble extracts expressing rErbB2_noTM were administered to BALB/c mice, specific rErbB2 immune responses were triggered. A potent antitumour activity was induced when vaccinated mice were challenged with syngeneic transplantable ErbB2(+) mammary carcinoma cells. To our knowledge, this is the first report of expression of rErbB2 in plants and of its efficacy in inducing a protective antitumour immune response, opening interesting perspectives for further immunological testing. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Analysis of gene expression profiles in tympanic membrane following perforation using PCR Array in rats--preliminary investigation.

PubMed

Hassmann-Poznańska, Elżbieta; Taranta, Andrzej; Bialuk, Izabela; Poznańska, Maria; Zajączkiewicz, Hanna; Winnicka, Maria Małgorzata

2013-10-01

The goal of this work was to identify genes, known to be involved in the skin wound healing, that express differentially in the healthy and injured tympanic membrane (TM), and designate the molecules potentially beneficial for treatment of TM perforation. The molecular mechanisms controlling the course of TM regeneration are far from being elucidated. Twenty rats had their tympanic membranes perforated, while four served as a control. Animals were sacrificed on either days 1, 2, 3, 5 and 10 post injury, and TMs were immediately dissected and frozen in liquid nitrogen. Total TM RNA was isolated and reversely transcribed. qPCR was performed using Rat Wound Healing RT(2) Profiler PCR Array (QIAGEN) containing primers for 84 genes. Statistically significant changes in the expression of 42 genes were found in various stages of TM healing. The increased expression of genes taking part in the inflammatory reaction (interleukin 6, granulocyte and macrophage chemotactic proteins) was observed from day 2. The expression of several genes of extracellular matrix components and their remodeling enzymes was also changed. Among growth factor genes: Vegfa, Igf1 and Hbegf showed increased expression at the beginning of the healing process, while Hgf expression was highest on day 3. Several changes in the expression of genes involved in remodeling of extracellular matrix point to important role of connective tissue in TM healing. The molecules accelerating this process, like HbEGF and HGF, seem to be good candidates for further evaluation of their possible use in clinical treatment. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species.

PubMed

Nguyen, Thao Thi; Lee, Hyun-Hee; Park, Jungwook; Park, Inmyoung; Seo, Young-Su

2017-04-01

As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representative Burkholderia species. The species comprised plant pathogens ( B. glumae BGR1, B. gladioli BSR3), human pathogens ( B. pseudomallei K96243, B. cepacia LO6), and plant-growth promoting endophytes ( Burkholderia sp. KJ006, B. phytofirmans PsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collected Burkholderia species using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, human-pathogenic, and endophytic bacteria.

Genetic variants in PNPLA3 and TM6SF2 predispose to the development of hepatocellular carcinoma in individuals with alcohol-related cirrhosis.

PubMed

Stickel, Felix; Buch, Stephan; Nischalke, Hans Dieter; Weiss, Karl Heinz; Gotthardt, Daniel; Fischer, Janett; Rosendahl, Jonas; Deltenre, Pierre; Marot, Astrid; Elamly, Mona; Casper, Markus; Lammert, Frank; McQuillin, Andrew; Zopf, Steffen; Spengler, Ulrich; Marhenke, Silke; Kirstein, Martha M; Vogel, Arndt; Eyer, Florian; von Felden, Johann; Wege, Henning; Buch, Thorsten; Schafmayer, Clemens; Braun, Felix; Berg, Thomas; Morgan, Marsha Y; Hampe, Jochen

2018-03-13

Variants in patatin-like phospholipase domain-containing 3 (PNPLA3; rs738409), transmembrane 6 superfamily member 2 (TM6SF2; rs58542926), and membrane bound O-acyltransferase domain containing 7 (MBOAT7; rs641738) are risk factors for the development of alcohol-related cirrhosis. Within this population, PNPLA3 rs738409 is also an established risk factor for the development of hepatocellular carcinoma (HCC). The aim of this study was to explore possible risk associations of TM6SF2 rs58542926 and MBOAT7 rs641738 with HCC. Risk variants in PNPLA3, TM6SF2, and MBOAT7 were genotyped in 751 cases with alcohol-related cirrhosis and HCC and in 1165 controls with alcohol-related cirrhosis without HCC. Association with the risk of developing HCC was analyzed using multivariate logistic regression. The development of HCC was independently associated with PNPLA3 rs738409 (OR adjusted 1.84 [95% CI 1.55-2.18], p = 1.85 × 10 -12 ) and TM6SF2 rs58542926 (OR adjusted 1.66 [1.30-2.13], p = 5.13 × 10 -05 ), using an additive model, and controlling the sex, age, body mass index, and type 2 diabetes mellitus; the risk associated with carriage of MBOAT7 rs641738 (OR adjusted 1.04 [0.88-1.24], p = 0.61) was not significant. The population-attributable fractions were 43.5% for PNPLA3 rs738409, 11.5% for TM6SF2 rs58542926, and 49.9% for the carriage of both the variants combined. Carriage of TM6SF2 rs58542926 is an additional risk factor for the development of HCC in people with alcohol-related cirrhosis. Carriage of both PNPLA3 rs738409 and TM6SF2 rs58542926 accounts for half of the attributable risk for HCC in this population. Genotyping will allow for more precise HCC risk-stratification of patients with alcohol-related cirrhosis, and genotype-guided screening algorithms would optimize patient care.

Internet use, online information seeking and knowledge among third molar patients attending public dental services.

PubMed

Hanna, K; Sambrook, P; Armfield, J M; Brennan, D S

2017-09-01

While Australians are searching the internet for third molar (TM) information, the usefulness of online sources may be questioned due to quality variation. This study explored: (i) internet use, online information-seeking behaviour among TM patients attending public dental services; and (ii) whether patients' TM knowledge scores are associated with the level of internet use and eHealth Literacy Scale (eHEALS) scores. Baseline survey data from the 'Engaging Patients in Decision-Making' study were used. Variables included: sociodemographics, internet access status, online information-seeking behaviour, eHEALS, the Control Preferences Scale (CPS) and TM knowledge. Participants (N = 165) were mainly female (73.8%), aged 19-25 years (42.4%) and had 'secondary school or less' education (58.4%). A majority (N = 79, 52.7%) had sought online dental information which was associated with active decisional control preference (odds ratio = 3.1, P = 0.034) and higher educational attainment (odds ratio = 2.7, P = 0.040). TM knowledge scores were not associated with either the level of internet use (F (2,152) = 2.1, P = 0.094, χ 2 = 0.0310) or the eHEALS scores (r = 0.147, P = 0.335). 'The internet-prepared patient' phenomena exists among public TM patients and was explained by preference for involvement in decision-making. However, internet use was not associated with better TM knowledge. Providing TM patients with internet guidance may be an opportunity to improve TM knowledge. © 2017 Australian Dental Association.

Comprehensive Analysis of the COBRA-Like (COBL) Gene Family in Gossypium Identifies Two COBLs Potentially Associated with Fiber Quality

PubMed Central

Niu, Erli; Shang, Xiaoguang; Cheng, Chaoze; Bao, Jianghao; Zeng, Yanda; Cai, Caiping; Du, Xiongming; Guo, Wangzhen

2015-01-01

COBRA-Like (COBL) genes, which encode a plant-specific glycosylphosphatidylinositol (GPI) anchored protein, have been proven to be key regulators in the orientation of cell expansion and cellulose crystallinity status. Genome-wide analysis has been performed in A. thaliana, O. sativa, Z. mays and S. lycopersicum, but little in Gossypium. Here we identified 19, 18 and 33 candidate COBL genes from three sequenced cotton species, diploid cotton G. raimondii, G. arboreum and tetraploid cotton G. hirsutum acc. TM-1, respectively. These COBL members were anchored onto 10 chromosomes in G. raimondii and could be divided into two subgroups. Expression patterns of COBL genes showed highly developmental and spatial regulation in G. hirsutum acc. TM-1. Of them, GhCOBL9 and GhCOBL13 were preferentially expressed at the secondary cell wall stage of fiber development and had significantly co-upregulated expression with cellulose synthase genes GhCESA4, GhCESA7 and GhCESA8. Besides, GhCOBL9 Dt and GhCOBL13 Dt were co-localized with previously reported cotton fiber quality quantitative trait loci (QTLs) and the favorable allele types of GhCOBL9 Dt had significantly positive correlations with fiber quality traits, indicating that these two genes might play an important role in fiber development. PMID:26710066

Molecular characterization of novel mucosotropic papillomaviruses from a Florida manatee (Trichechus manatus latirostris).

PubMed

2015-12-01

We isolated two new manatee papillomavirus (PV) types, TmPV3 and TmPV4, from a Florida manatee (Trichechus manatus latirostris). Two PV types were previously isolated from this species. TmPV1 is widely dispersed amongst manatees and a close-to-root PV; not much is known about TmPV2. The genomes of TmPV3 and TmPV4 were 7622 and 7771 bp in size, respectively. Both PVs had a genomic organization characteristic of all PVs, with one non-coding region and seven ORFs, including the E7 ORF that is absent in other cetacean PVs. Although these PVs were isolated from separate genital lesions of the same manatee, an enlarged E2/E4 ORF was found only in the TmPV4 genome. The full genome and L1 sequence similarities between TmPV3 and TmPV4 were 63.2 and 70.3 %, respectively. These genomes shared only 49.1 and 50.2 % similarity with TmPV1. The pairwise alignment of L1 nucleotide sequences indicated that the two new PVs nested in a monophyletic group of the genus Rhopapillomavirus, together with the cutaneotropic TmPV1 and TmPV2.

Investigations of vegetation and soils information contained in LANDSAT Thematic Mapper and Multispectral Scanner data

NASA Technical Reports Server (NTRS)

Crist, E. P.; Laurin, R.; Colwell, J. E.; Kauth, R. J.

1984-01-01

An extension of the TM tasseled cap transformation to reflectance factor data is presented, and the basic concepts underlying the tasseled cap transformations are described. The ratio of TM bands 5 and 7, and TM tasseled cap wetness, are both shown to offer promise of direct detection of available soil moisture. Some effects of organic matter and other soil characteristics or constituents on TM tasseled cap spectral response are also considered.

BOREAS RSS-7 Landsat TM LAI IMages of the SSA and NSA

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Nickeson, Jaime (Editor); Chen, Jing; Cihlar, Josef

2000-01-01

The BOReal Ecosystem-Atmosphere Study Remote Sensing Science (BOREAS RSS-7) team used Landsat Thematic Mapper (TM) images processed at CCRS to produce images of Leaf Area Index (LAI) for the BOREAS study areas. Two images acquired on 06-Jun and 09-Aug-1991 were used for the SSA, and one image acquired on 09-Jun-1994 was used for the NSA. The LAI images are based on ground measurements and Landsat TM Reduced Simple Ratio (RSR) images. The data are stored in binary image-format files.

Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi

USDA-ARS?s Scientific Manuscript database

One result of the recent phylogenetically based rejection of the phylum Zygomycota was the description of the subphylum Entomophthoromycotina (not assigned to any phylum) for fungi traditionally treated in the order Entomophthorales. More extensive gene-based analyses of these fungi suggest that the...

Comparison of energy expenditure on a treadmill vs. an elliptical device at a self-selected exercise intensity.

PubMed

Brown, Gregory A; Cook, Chad M; Krueger, Ryan D; Heelan, Kate A

2010-06-01

Treadmills (TM) and elliptical devices (EL) are popular forms of exercise equipment. The differences in the training stimulus presented by TM or EL are unknown. The purpose of this investigation was to evaluate oxygen consumption, energy expenditure, and heart rate on a TM or EL when persons exercise at the same perceived level of exertion. After measuring peak oxygen uptake (VO2peak) in 9 male and 9 female untrained college-aged participants, the subjects performed 2 separate 15-minute submaximal exercise tests on the TM and EL at a rating of perceived exertion (RPE) of 12-13. VO2peak was higher (p<0.05) in the males (48.6+/-1.5 vs. 45.2+/-1.6 ml/kg/min) than the females (41.7+/-1.8 vs. 38.8+/-2.2 ml/kg/min) for both TM and EL (means+/-standard error of the mean; for TM vs. EL respectively), but there were no differences in the measured VO2peak between TM or EL. During submaximal exercise there were no differences in RPE between TM and EL. Total oxygen consumption was higher (p<0.05) in males (30.8+/-2.2 vs. 34.9+/-2.2 L) than females (24.1+/-1.8 vs. 26.9+/-1.7 L) but did not differ between TM and EL. Energy expenditure was not different between TM (569+/-110 J) or EL (636+/-120 kJ). Heart rate was higher (p<0.05) on the EL (164+/-16 beats/min) compared to the TM (145+/-15 beats/min). When subjects exercise at the same RPE on TM or EL, oxygen consumption and energy expenditure are similar in spite of a higher heart rate on the EL. These data indicate that during cross training or noncompetition-specific exercise, an elliptical device is an acceptable alternative to a treadmill.

A novel prolyl hydroxylase inhibitor protects against cell death after hypoxia.

PubMed

Kontani, Satoru; Nagata, Eiichiro; Uesugi, Tsuyoshi; Moriya, Yusuke; Fujii, Natsuko; Miyata, Toshio; Takizawa, Shunya

2013-12-01

Hypoxia-inducible factor 1 (HIF-1) is regulated by the oxygen-dependent hydroxylation of proline residues by prolyl hydroxylases (PHDs). We recently developed a novel PHD inhibitor, TM6008, that suppresses the activity of PHDs, inducing continuous HIF-1α activation. In this study, we investigated how TM6008 affects cell survival after hypoxic conditions capable of inducing HIF-1α expression and how TM6008 regulates PHDs and genes downstream of HIF-1α. After SHSY-5Y cells had been subjected to hypoxia, TM6008 was added to the cell culture medium under normoxic conditions. Apoptotic cell death was significantly augmented just after the hypoxic conditions, compared with cell death under normoxic conditions. Notably, when TM6008 was added to the media after the cells had been subjected to hypoxia, the expression level of HIF-1α increased and the number of cell deaths decreased, compared with the results for cells cultured in media without TM6008 after hypoxia, during the 7-day incubation period under normoxic conditions. Moreover, the protein expression levels of heme oxygenase 1, erythropoietin, and glucose transporter-3, which were genes downstream of HIF-1α, were elevated in media to which TM6008 had been added, compared with media without TM6008, during the 7-day incubation period under normoxic conditions. However, the protein expression levels of PHD2 and p53 which suppressed cell proliferation were suppressed in the media to which TM6008 had been added. Thus, TM6008, which suppresses the protein expressions of PHD2 and p53, might play an important role in cell survival after hypoxic conditions, with possible applications as a new compound for treatment after ischemic stroke.

66.7-keV γ -line intensity of 171Tm determined via neutron activation

NASA Astrophysics Data System (ADS)

Weigand, M.; Heftrich, T.; Düllmann, Ch. E.; Eberhardt, K.; Fiebiger, S.; Glorius, J.; Göbel, K.; Haas, R.; Langer, C.; Lohse, S.; Reifarth, R.; Renisch, D.; Wolf, C.

2018-03-01

Background: About 50% of the heavy elements are produced in stars during the slow neutron capture process. The analysis of branching points allows to set constraints on the temperature and the neutron density in the interior of stars. The temperature dependence of the branch point 171Tm is weak. Hence, the 171Tm neutron capture cross section can be used to constrain the neutron density during the main component of the s process in thermally pulsing asymptotic giant branch stars. Purpose: In order to perform neutron capture experiments on 171Tm, sample material has to be produced and characterized. The characterization is done by γ spectroscopy, relying on the intensities of the involved γ lines. Only the 66.7-keV γ line can be observed whose intensity was uncertain so far. Method: An enriched 170Er sample was activated with thermal neutrons at the TRIGA (Training, Research, Isotopes, General Atomics) research reactor at the Johannes Gutenberg-Universität Mainz. The activation resulted in an easily quantifiable number of 171Er nuclei that subsequently decayed to 171Tm. Result: The intensity of the 66.7-keV γ line of the 171Tm decay was measured to Iγ=(0.144 ±0.010 )% . Conclusions: Our result is in good agreement with the value found in the literature.

AGOR 28: SIO Shipyard Representative Bi-Weekly Progress Report

DTIC Science & Technology

2014-03-13

652/0 AGOR27 A055 TM Report - COMMERCIAL TECHNICAL MANUALS AND SUPPLEMENTAL DATA ( #368 DI-055 (TM) for 555c Kidde Fire Systems Fuel Shunt System ...TM) for 521 Fire Main System High-Level Manual) (R/ASR) 763/0 AGOR27 A055 TM Report - COMMERCIAL TECHNICAL MANUALS AND SUPPLEMENTAL DATA ( #384...Report - SINGLE SYSTEM VENDOR (SSV) DESIGN REVIEW AGENDAS AND MINUTES ( SSV #7 MINUTES AND SIGN-IN SHEET) (R/ASR) 47/0 AGOR27 A027- 41 DWG Report

Quasi four-level Tm:LuAG laser

NASA Technical Reports Server (NTRS)

Jani, Mahendra G. (Inventor); Barnes, Norman P. (Inventor); Hutcheson, Ralph L. (Inventor); Rodriguez, Waldo J. (Inventor)

1997-01-01

A quasi four-level solid-state laser is provided. A laser crystal is disposed in a laser cavity. The laser crystal has a LuAG-based host material doped to a final concentration between about 2% and about 7% thulium (Tm) ions. For the more heavily doped final concentrations, the LuAG-based host material is a LuAG seed crystal doped with a small concentration of Tm ions. Laser diode arrays are disposed transversely to the laser crystal for energizing the Tm ions.

One-Pot Synthesis of Lithium-Rich Cathode Material with Hierarchical Morphology.

PubMed

Luo, Kun; Roberts, Matthew R; Hao, Rong; Guerrini, Niccoló; Liberti, Emanuela; Allen, Christopher S; Kirkland, Angus I; Bruce, Peter G

2016-12-14

Lithium-rich transition metal oxides, Li 1+x TM 1-x O 2 (TM, transition metal), have attracted much attention as potential candidate cathode materials for next generation lithium ion batteries because their high theoretical capacity. Here we present the synthesis of Li[Li 0.2 Ni 0.2 Mn 0.6 ]O 2 using a facile one-pot resorcinol-formaldehyde method. Structural characterization indicates that the material adopts a hierarchical porous morphology consisting of uniformly distributed small pores and disordered large pore structures. The material exhibits excellent electrochemical cycling stability and a good retention of capacity at high rates. The material has been shown to be both advantageous in terms of gravimetric and volumetric capacities over state of the art commercial cathode materials.

Bracket debonding by mid-infrared laser radiation

NASA Astrophysics Data System (ADS)

Jelínková, H.; Šulc, J.; Dostálová, T.; Koranda, P.; Němec, M.; Hofmanova, P.

2009-03-01

The purpose of the study was to determine the proper laser radiation for ceramic bracket debonding and the investigation of the tooth root temperature injury. The debonding was investigated by diode-pumped continuously running Tm:YAP and Nd:YAG lasers, and by GaAs laser diode generating radiation with the wavelengths 1.997 μm, 1.444 μm, and 0.808 μm, respectively. The possibility of brackets removal by laser radiation was investigated together with the tooth and, it specifically, root temperature rise. From the results it follows that continuously running diode pumped Tm:YAG or Nd:YAG laser generating wavelengths 1.997 μm or 1.444 μm, respectively, having the output power 1 W can be good candidates for ceramic brackets debonding.

Functional role of oligomerization for bacterial and plant SWEET sugar transporter family.

PubMed

Xuan, Yuan Hu; Hu, Yi Bing; Chen, Li-Qing; Sosso, Davide; Ducat, Daniel C; Hou, Bi-Huei; Frommer, Wolf B

2013-09-24

Eukaryotic sugar transporters of the MFS and SWEET superfamilies consist of 12 and 7 α-helical transmembrane domains (TMs), respectively. Structural analyses indicate that MFS transporters evolved from a series of tandem duplications of an ancestral 3-TM unit. SWEETs are heptahelical proteins carrying a tandem repeat of 3-TM separated by a single TM. Here, we show that prokaryotes have ancestral SWEET homologs with only 3-TM and that the Bradyrhizobium japonicum SemiSWEET1, like Arabidopsis SWEET11, mediates sucrose transport. Eukaryotic SWEETs most likely evolved by internal duplication of the 3-TM, suggesting that SemiSWEETs form oligomers to create a functional pore. However, it remains elusive whether the 7-TM SWEETs are the functional unit or require oligomerization to form a pore sufficiently large to allow for sucrose passage. Split ubiquitin yeast two-hybrid and split GFP assays indicate that Arabidopsis SWEETs homo- and heterooligomerize. We examined mutant SWEET variants for negative dominance to test if oligomerization is necessary for function. Mutation of the conserved Y57 or G58 in SWEET1 led to loss of activity. Coexpression of the defective mutants with functional A. thaliana SWEET1 inhibited glucose transport, indicating that homooligomerization is necessary for function. Collectively, these data imply that the basic unit of SWEETs, similar to MFS sugar transporters, is a 3-TM unit and that a functional transporter contains at least four such domains. We hypothesize that the functional unit of the SWEET family of transporters possesses a structure resembling the 12-TM MFS structure, however, with a parallel orientation of the 3-TM unit.

Functional role of oligomerization for bacterial and plant SWEET sugar transporter family

PubMed Central

Xuan, Yuan Hu; Hu, Yi Bing; Chen, Li-Qing; Sosso, Davide; Ducat, Daniel C.; Hou, Bi-Huei; Frommer, Wolf B.

2013-01-01

Eukaryotic sugar transporters of the MFS and SWEET superfamilies consist of 12 and 7 α-helical transmembrane domains (TMs), respectively. Structural analyses indicate that MFS transporters evolved from a series of tandem duplications of an ancestral 3-TM unit. SWEETs are heptahelical proteins carrying a tandem repeat of 3-TM separated by a single TM. Here, we show that prokaryotes have ancestral SWEET homologs with only 3-TM and that the Bradyrhizobium japonicum SemiSWEET1, like Arabidopsis SWEET11, mediates sucrose transport. Eukaryotic SWEETs most likely evolved by internal duplication of the 3-TM, suggesting that SemiSWEETs form oligomers to create a functional pore. However, it remains elusive whether the 7-TM SWEETs are the functional unit or require oligomerization to form a pore sufficiently large to allow for sucrose passage. Split ubiquitin yeast two-hybrid and split GFP assays indicate that Arabidopsis SWEETs homo- and heterooligomerize. We examined mutant SWEET variants for negative dominance to test if oligomerization is necessary for function. Mutation of the conserved Y57 or G58 in SWEET1 led to loss of activity. Coexpression of the defective mutants with functional A. thaliana SWEET1 inhibited glucose transport, indicating that homooligomerization is necessary for function. Collectively, these data imply that the basic unit of SWEETs, similar to MFS sugar transporters, is a 3-TM unit and that a functional transporter contains at least four such domains. We hypothesize that the functional unit of the SWEET family of transporters possesses a structure resembling the 12-TM MFS structure, however, with a parallel orientation of the 3-TM unit. PMID:24027245

Hunting for the function of orphan GPCRs – beyond the search for the endogenous ligand

PubMed Central

Ahmad, Raise; Wojciech, Stefanie; Jockers, Ralf

2015-01-01

Seven transmembrane-spanning proteins (7TM), also called GPCRs, are among the most versatile and evolutionary successful protein families. Out of the 400 non-odourant members identified in the human genome, approximately 100 remain orphans that have not been matched with an endogenous ligand. Apart from the classical deorphanization strategies, several alternative strategies provided recent new insights into the function of these proteins, which hold promise for high therapeutic potential. These alternative strategies consist of the phenotypical characterization of organisms silenced or overexpressing orphan 7TM proteins, the search for constitutive receptor activity and formation of protein complexes including 7TM proteins as well as the development of synthetic, surrogate ligands. Taken together, a variety of ligand-independent functions can be attributed to orphan 7TM proteins that range from constitutive activity to complex formation with other proteins and include ‘true’ orphans for which no ligand exist and ‘conditional’ orphans that behave like orphans in the absence of ligand and as non-orphans in the presence of ligand. PMID:25231237

Effect of surface coating of KYb2F7:Tm3+ on optical properties and biomedical applications

NASA Astrophysics Data System (ADS)

Pedraza, Francisco J.; Avalos, Julio C.; Yust, Brian G.; Tsin, Andrew; Sardar, Dhiraj K.

2016-09-01

This project aims to provide an insight on the effects of biocompatible polymers on the optical properties and the nanoparticle-cell interaction of KYb2F7:Tm3+ nanocrystals that exhibit strong near infrared (NIR) fluorescence. KYb2F7:Tm3+ nanocrystals were synthesized with a diameter of 20-30 nm and surface modified with poly(ethylene glycol), Pluronic® F-127, and poly(N-vinylpyrrolidone), due to the associated advantages. Some of these include biocompatibility and biodistribution in the instance of agglomeration and hydrophobicity as well as the addition of a targeting agent and drug loading by further functionalization. Despite the decrease in fluorescence intensity induced by the surface modification, thulium’s emission fingerprint was easily detected. Moreover, surface modified KYb2F7:Tm3+ nanocrystals failed to induce a toxic response on endothelial cells following a 24 h uptake period up to concentrations of 100 μg ml-1. In vitro toxicity and confocal imaging have demonstrated the versatility of these NIR fluorescence nanocrystals in biomedical imaging, drug delivery, and photodynamic therapy.

Chemical bond parameters and photoluminescence of a natural-white-light Ca{sub 9}La(VO{sub 4}){sub 7}:Tm{sup 3+},Eu{sup 3+} with one O{sup 2−}→V{sup 5+} charge transfer and dual f-f transition emission centers

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

Li, Ling; Liu, Xiao Guang; Department of Physics, Pukyong National University, Busan 608-737

2015-01-15

The relationship between the photoluminescence properties and the crystal structure of undoped, Eu{sup 3+} or/ and Tm{sup 3+} singly or codoped Ca{sub 9}La(VO{sub 4}){sub 7} (CLaVO) samples was discussed. Under the excitation of UV light, CLaVO:Tm{sup 3+}, CLaVO, and CLaVO:Eu{sup 3+} exhibit the characteristic emissions of Tm{sup 3+} ({sup 1}G{sub 4}→{sup 3}H{sub 6}, blue), O{sup 2−}→V{sup 5+} charge transfer (CT), and Eu{sup 3+} ({sup 5}D{sub 0}→{sup 7}F{sub 2}, red), respectively. By adjusting the doping concentration of Tm{sup 3+} and Eu{sup 3+} ions in CLaVO, a natural white emission in a single composition with the color temperature at 6181 K wasmore » obtained. Based on the dielectric theory of complex crystal, the chemical bond parameters of La-O and V-O bonds were quantitatively calculated. The standard deviation of environmental factor of every bond (EFSD), which can be expressed as σ(h{sub e{sub i}})=√((1/N)∑{sub i=1}{sup N}(h{sub e{sub i}}−μ){sup 2}) (h{sub e{sub i}}=(f{sub c{sub i}}α{sub b{sub i}}){sup 1/2}Q{sub B{sub i}} and μ=(1/N)∑{sub i=1}{sup N}h{sub e{sub i}}), was proposed to quantitatively express the distortion degree of VO{sub 4}{sup 3−} from that of an ideal tetrahedron. The maximum change of EFSD comes from the [VO{sub 4}]{sup −} tetrahedra in CLaVO sample by comparison with that of EFSD of isostructural Ca{sub 9}Gd(VO{sub 4}){sub 7}. This is possible the key reason that the undoped CLaVO sample has self-activated emission while the self-activated emission of its isostructural Ca{sub 9}Gd(VO{sub 4}){sub 7} sample cannot be found. The quantitative calculation also demonstrated that the broad excitation bands at 319 nm in CLaVO:Tm and at 335 nm in CLaVO:Eu were due to the O-V2 and O-V3 (overlap with O-V2) CT, not the CT energy of O{sup 2−}-Eu1{sup 3+} (O{sup 2−}-Tm1{sup 3+}), O{sup 2−}-Eu2{sup 3+} (O{sup 2−}-Tm2{sup 3+}), and O{sup 2−}-Eu3{sup 3+} (O{sup 2−}-Tm3{sup 3+}). The environmental factors surrounding the atoms V1, V2 and V3 were calculated to be 1.577, 1.6379 and 1.7554, respectively. It can be demonstrated that the excitation spectra at 319 nm for CLaVO:Tm and 335 nm for CLaVO:Eu came from the O-V2 and O-V3 CT, respectively. - Graphical abstracts: The relationship between the photoluminescence properties and the crystal structure of undoped, Eu{sup 3+} or/ and Tm{sup 3+} singly or codoped Ca{sub 9}La(VO{sub 4}){sub 7} (CLaVO) samples was discussed experimentally and theoretically. - Highlights: ●The photoluminescence properties of Ca{sub 9}La(VO{sub 4}){sub 7}:Eu, Tm were measured. ●The tunable color including white emission can be obtained. ●The important chemical bond parameters of O-V were calculated quantitatively. ●The standard deviation of environmental factor of every bond was proposed. ●The theoretical analysis of the self-activated emission for Ca{sub 9}La(VO{sub 4}){sub 7} was given.« less

Optical image modulation above the submarine bottom topography: a case study on the Taiwan Banks, China

NASA Astrophysics Data System (ADS)

Li, Yan; Hu, Jianyu; Li, Jing; Fu, Bin; Ma, Liming

2003-05-01

A possible mechanism to explain the correlation between submarine topography and the direct sunlight specially reflected from the sea surface with variable roughness caused by the bottom-current effect was suggested fifteen years ago by Henning et al. in International Journal of Remote Sensing, 9, 45-67, after comparing radar satellite image and Skylab satellite photograph of the North American east coast (Nantucket Shoals) with submarine relief features. A case study is carried out in the famous sand waves field located at the Taiwan banks of Taiwan Strait in August 1998. The TM images, either visible bands (TM1, TM2, TM3) or near infrared bands (TM4, TM5, TM7), shows submarine relief features for sand waves, with wavelength of 300 to 2000 meters, riding on the lager scale sand ridges and channel system. Sea truth data including 660 nm beam attenuation coefficient profiles were conducted in the same period. We compare signals of TM images, attenuation coefficient profiles, and sounding maps of the Taiwan Bands. The subsurface upwelling signals with contributions of the water column and the bottom, either estimated by single or quasi-single-scattering theory or revealed by the TM images after removing the contribution of direct sunlight reflected signals from sea surface, were too weak to distinguish the ridges and troughs of bedforms especially for red and near infrared bands. However, the direct sunlight specially reflected signals from the sea surface, approximately at same level in water-leaving reflectance not only for visible bands (TM1, TM2, TM3) but also for near infrared bands (TM4, TM5, TM7), was the major submarine bottom topography signals especially for those pixels towards the direction of the sun azimuth. Following a physical description for the lee waves appeared on free surface when the current flows round an underwater obstacle, the direct sunlight reflected signals related wave face slope, is dominated by the height and depth of sand waves and sand ridges, and current speed of the flows over those bedforms. The direct sunlight reflected signals from the sea surface could be regarded as a powerful tool to detect bedforms and other underwater obstacles.

Nanogel-based natural polymers as smart carriers for the controlled delivery of Timolol Maleate through the cornea for glaucoma.

PubMed

Ilka, Roya; Mohseni, Mojdeh; Kianirad, Mehran; Naseripour, Masood; Ashtari, Khadijeh; Mehravi, Bita

2018-04-01

Despite frequent scientific efforts, efficient ocular drug delivery is a major challenge for pharmaceutical scientists. Poor bioavailability of ophthalmic solutions can be overcome by using smart ophthalmic drug-delivery systems. In this research, loading and delivery of Timolol Maleate (TM) through the cornea by synthesized nanoparticles based on biopolymers (chitosan-alginate) were studied. The physico-chemical properties of these nanoparticles were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM) and dynamic light scattering (DLS). Loading and release were evaluated by a UV-vis spectrometer and the ex vivo permeation study was carried out using the Franz Diffusion Cell and fluorescent microscopy studies. The results indicated that morphology and size of nanoparticles were spherical and in the range of 80-100nm. The loading capacity and encapsulation efficiency were about 42% and 94% respectively. They illustrated a burst release in the first hour followed by a slower and more sustained drug release during the next 24h. Also, the results indicated that the cornea penetration of TM loaded in nanoparticles was twice than that of TM. Hence, this nanocarrier can be considered as a suitable candidate for controlled TM delivery and release through the cornea. Copyright © 2017 Elsevier B.V. All rights reserved.

Barcoding Sponges: An Overview Based on Comprehensive Sampling

PubMed Central

Vargas, Sergio; Schuster, Astrid; Sacher, Katharina; Büttner, Gabrielle; Schätzle, Simone; Läuchli, Benjamin; Hall, Kathryn; Hooper, John N. A.; Erpenbeck, Dirk; Wörheide, Gert

2012-01-01

Background Phylum Porifera includes ∼8,500 valid species distributed world-wide in aquatic ecosystems ranging from ephemeral fresh-water bodies to coastal environments and the deep-sea. The taxonomy and systematics of sponges is complicated, and morphological identification can be both time consuming and erroneous due to phenotypic convergence and secondary losses, etc. DNA barcoding can provide sponge biologists with a simple and rapid method for the identification of samples of unknown taxonomic membership. The Sponge Barcoding Project (www.spongebarcoding.org), the first initiative to barcode a non-bilaterian metazoan phylum, aims to provide a comprehensive DNA barcode database for Phylum Porifera. Methodology/Principal Findings ∼7,400 sponge specimens have been extracted, and amplification of the standard COI barcoding fragment has been attempted for approximately 3,300 museum samples with ∼25% mean amplification success. Based on this comprehensive sampling, we present the first report on the workflow and progress of the sponge barcoding project, and discuss some common pitfalls inherent to the barcoding of sponges. Conclusion A DNA-barcoding workflow capable of processing potentially large sponge collections has been developed and is routinely used for the Sponge Barcoding Project with success. Sponge specific problems such as the frequent co-amplification of non-target organisms have been detected and potential solutions are currently under development. The initial success of this innovative project have already demonstrated considerable refinement of sponge systematics, evaluating morphometric character importance, geographic phenotypic variability, and the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum). PMID:22802937

Transmission electron microscopy study of the MgS–Tm{sub 2}S{sub 3} system

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

Varadé-López, R., E-mail: rebeca.varade@ucm.es; Ávila-Brande, D., E-mail: davilabr@ucm.es; Urones-Garrote, E., E-mail: esteban.urones@pdi.ucm.es

2015-09-15

This work presents the structural–microstructural characterization of the NaCl-derivative MgS–Tm{sub 2}S{sub 3} system, which can be formulated by the expression Mg{sub (1−x)}Tm{sub (2/3)x}□{sub (1/3)x}S (□→cation vacancy). Transmission electron microscopy observations show the transition between NaCl-type and spinel-type structures when 0 ≤x≤ 0.75. The increase of Tm content in the solid solution provokes the increase of the spinel-type phase proportion, which intergrows with the NaCl-type crystals. When x≥0.75, some phases derived from NaCl-type structure through the chemical twinning at the unit cell level crystallographic operation are observed, such as CT-MgTm{sub 2}S{sub 4} and CT-MgTm{sub 4}S{sub 7}. The existence and nature ofmore » the extended defects observed along the c direction of these structures are characterized by means of Scanning-Transmission electron microscopy high-angle dark field imaging, which allows observing the presence of quasi ordered crystals with new possible complex stoichiometries at atomic resolution. - Graphical abstract: HAADF-STEM image of a disordered CT-MgYb{sub 2}S{sub 4} crystal. The disordered twin-slab sequences are marked by arrows. - Highlights: • Structural evolution of the Mg{sub (1−x)}Tm{sub (2/3)x}□{sub (1/3)x}S system was characterized by means of TEM. • The increase in Tm content provokes the transition from NaCl to spinel-type structure up to x=0.75. • Chemical twinned phases CT-MgTm{sub 2}S{sub 4} and CT-MgTm{sub 4}S{sub 7} are observed at high Tm contents. • Extended defects in CT-crystals are characterized with atomic resolution STEM-HAADF images.« less

Strong and multi-antigen specific immunity by hepatitis B core antigen (HBcAg)-based vaccines in a murine model of chronic hepatitis B: HBcAg is a candidate for a therapeutic vaccine against hepatitis B virus.

PubMed

Akbar, Sheikh Mohammad Fazle; Chen, Shiyi; Al-Mahtab, Mamun; Abe, Masanori; Hiasa, Yoichi; Onji, Morikazu

2012-10-01

Experimental evidence suggests that hepatitis B core antigen (HBcAg)-specific cytotoxic T lymphocytes (CTL) are essential for the control of hepatitis B virus (HBV) replication and prevention of liver damage in patients with chronic hepatitis B (CHB). However, most immune therapeutic approaches in CHB patients have been accomplished with hepatitis B surface antigen (HBsAg)-based prophylactic vaccines with unsatisfactory clinical outcomes. In this study, we prepared HBsAg-pulsed dendritic cells (DC) and HBcAg-pulsed DC by culturing spleen DC from HBV transgenic mice (HBV TM) and evaluated the immunomodulatory capabilities of these antigens, which may serve as a better therapy for CHB. The kinetics of HBsAg, antibody levels against HBsAg (anti-HBs), proliferation of HBsAg- and HBcAg-specific lymphocytes, production of antigen-specific CTL, and activation of endogenous DC were compared between HBV TM vaccinated with either HBsAg- or HBcAg-pulsed DC. Vaccination with HBsAg-pulsed DC induced HBsAg-specific immunity, but failed to induce HBcAg-specific immunity in HBV TM. However, immunization of HBV TM with HBcAg-pulsed DC resulted in: (1) HBsAg negativity, (2) production of anti-HBs, and (3) development of HBsAg- and HBcAg-specific T cells and CTL in the spleen and the liver. Additionally, significantly higher levels of activated endogenous DC were detected in HBV TM immunized with HBcAg-pulsed DC compared to HBsAg-pulsed DC (p<0.05). The capacity of HBcAg to modulate both HBsAg- and HBcAg-specific immunity in HBV TM, and activation of endogenous DC in HBV TM without inducing liver damage suggests that HBcAg should be an integral component of the therapeutic vaccine against CHB. Copyright © 2012 Elsevier B.V. All rights reserved.

Cox4i2, Ifit2, and Prdm11 Mutant Mice: Effective Selection of Genes Predisposing to an Altered Airway Inflammatory Response from a Large Compendium of Mutant Mouse Lines.

PubMed

Horsch, Marion; Aguilar-Pimentel, Juan Antonio; Bönisch, Clemens; Côme, Christophe; Kolster-Fog, Cathrine; Jensen, Klaus T; Lund, Anders H; Lee, Icksoo; Grossman, Lawrence I; Sinkler, Christopher; Hüttemann, Maik; Bohn, Erwin; Fuchs, Helmut; Ollert, Markus; Gailus-Durner, Valérie; de Angelis, Martin Hrabĕ; Beckers, Johannes

2015-01-01

We established a selection strategy to identify new models for an altered airway inflammatory response from a large compendium of mutant mouse lines that were systemically phenotyped in the German Mouse Clinic (GMC). As selection criteria we included published gene functional data, as well as immunological and transcriptome data from GMC phenotyping screens under standard conditions. Applying these criteria we identified a few from several hundred mutant mouse lines and further characterized the Cox4i2tm1Hutt, Ifit2tm1.1Ebsb, and Prdm11tm1.1ahl lines following ovalbumin (OVA) sensitization and repeated OVA airway challenge. Challenged Prdm11tm1.1ahl mice exhibited changes in B cell counts, CD4+ T cell counts, and in the number of neutrophils in bronchoalveolar lavages, whereas challenged Ifit2tm1.1Ebsb mice displayed alterations in plasma IgE, IgG1, IgG3, and IgM levels compared to the challenged wild type littermates. In contrast, challenged Cox4i2tm1Hutt mutant mice did not show alterations in the humoral or cellular immune response compared to challenged wild type mice. Transcriptome analyses from lungs of the challenged mutant mouse lines showed extensive changes in gene expression in Prdm11tm1.1ahl mice. Functional annotations of regulated genes of all three mutant mouse lines were primarily related to inflammation and airway smooth muscle (ASM) remodeling. We were thus able to define an effective selection strategy to identify new candidate genes for the predisposition to an altered airway inflammatory response under OVA challenge conditions. Similar selection strategies may be used for the analysis of additional genotype-envirotype interactions for other diseases.

Cox4i2, Ifit2, and Prdm11 Mutant Mice: Effective Selection of Genes Predisposing to an Altered Airway Inflammatory Response from a Large Compendium of Mutant Mouse Lines

PubMed Central

Bönisch, Clemens; Côme, Christophe; Kolster-Fog, Cathrine; Jensen, Klaus T.; Lund, Anders H.; Lee, Icksoo; Grossman, Lawrence I.; Sinkler, Christopher; Hüttemann, Maik; Bohn, Erwin; Fuchs, Helmut; Ollert, Markus; Gailus-Durner, Valérie; Hrabĕ de Angelis, Martin; Beckers, Johannes

2015-01-01

We established a selection strategy to identify new models for an altered airway inflammatory response from a large compendium of mutant mouse lines that were systemically phenotyped in the German Mouse Clinic (GMC). As selection criteria we included published gene functional data, as well as immunological and transcriptome data from GMC phenotyping screens under standard conditions. Applying these criteria we identified a few from several hundred mutant mouse lines and further characterized the Cox4i2tm1Hutt, Ifit2tm1.1Ebsb, and Prdm11tm1.1ahl lines following ovalbumin (OVA) sensitization and repeated OVA airway challenge. Challenged Prdm11tm1.1ahl mice exhibited changes in B cell counts, CD4+ T cell counts, and in the number of neutrophils in bronchoalveolar lavages, whereas challenged Ifit2tm1.1Ebsb mice displayed alterations in plasma IgE, IgG1, IgG3, and IgM levels compared to the challenged wild type littermates. In contrast, challenged Cox4i2tm1Hutt mutant mice did not show alterations in the humoral or cellular immune response compared to challenged wild type mice. Transcriptome analyses from lungs of the challenged mutant mouse lines showed extensive changes in gene expression in Prdm11tm1.1ahl mice. Functional annotations of regulated genes of all three mutant mouse lines were primarily related to inflammation and airway smooth muscle (ASM) remodeling. We were thus able to define an effective selection strategy to identify new candidate genes for the predisposition to an altered airway inflammatory response under OVA challenge conditions. Similar selection strategies may be used for the analysis of additional genotype – envirotype interactions for other diseases. PMID:26263558

Anaysis of the quality of image data required by the LANDSAT-4 Thematic Mapper and Multispectral Scanner. [agricultural and forest cover types in California

NASA Technical Reports Server (NTRS)

Colwell, R. N. (Principal Investigator)

1984-01-01

The spatial, geometric, and radiometric qualities of LANDSAT 4 thematic mapper (TM) and multispectral scanner (MSS) data were evaluated by interpreting, through visual and computer means, film and digital products for selected agricultural and forest cover types in California. Multispectral analyses employing Bayesian maximum likelihood, discrete relaxation, and unsupervised clustering algorithms were used to compare the usefulness of TM and MSS data for discriminating individual cover types. Some of the significant results are as follows: (1) for maximizing the interpretability of agricultural and forest resources, TM color composites should contain spectral bands in the visible, near-reflectance infrared, and middle-reflectance infrared regions, namely TM 4 and TM % and must contain TM 4 in all cases even at the expense of excluding TM 5; (2) using enlarged TM film products, planimetric accuracy of mapped poins was within 91 meters (RMSE east) and 117 meters (RMSE north); (3) using TM digital products, planimetric accuracy of mapped points was within 12.0 meters (RMSE east) and 13.7 meters (RMSE north); and (4) applying a contextual classification algorithm to TM data provided classification accuracies competitive with Bayesian maximum likelihood.

Purification of a myotoxin from the toadfish Thalassophryne maculosa (Günter) venom.

PubMed

Sosa-Rosales, J I; D'Suze, G; Salazar, V; Fox, J; Sevcik, C

2005-02-01

Venom was milked by gently pressing the base of the opercular and dorsal fin spines. Three fractions were obtained by molecular exclusion high pressure liquid chromatography (HPLC) (Protein Pak 125SW, Millipore Corporation) column, but only the last one with 22.7 min retention time (rt) was biological active (TmPP-22.7). This fraction was rechromatographed on reversed phase HPLC chlorobutylsilane columns (C4, Vydac) nine fractions were obtained, but only one (TmC4-47.2) with 47.2 min rt was biologically active. MALD-TOF mass analysis was carried out on two samples of TmC-47.2 and the results were 15,161.36 and 15,154.70 a.m.u., respectively. Raw venom (1040 microg/ml) depolarised frog (Hyla crepitans) muscle irreversibly from -85 (-88, -81) mV (n=20, median and its 95% CI) to -18 (-24, -15) mV (n=24). The biological activity in TmPP-22.7 (38 microg/ml), which depolarised muscle fibres from -79 (-82, -76) mV (n=20) to -63 (-69 -57) mV (n=24). The depolarising fraction was TmC4-47.2 (50 microg/ml) which depolarised muscles from -87 (91, -82) mV (n=33) to -63 (-76 -51) mV (n=53); the depolarising effect at this concentration was completely reversed on washing with normal saline for 2 h. Muscles treated with 1 microM tetrodotoxin (TTX) were depolarised from -80 (-85, -72) mV (n=49) to -44 (-56, -31) mV (n=44) when 100 microg/ml TmC4-47.2 were applied with TTX; washing 130 min with 1 microM TTX repolarised to -59 (-69, -50) mV (n=25). We also present evidence that TmC4-47.2 induces myonecrosis in mice.

Analysis of chemical equilibrium of silicon-substituted fluorescein and its application to develop a scaffold for red fluorescent probes.

PubMed

Hirabayashi, Kazuhisa; Hanaoka, Kenjiro; Takayanagi, Toshio; Toki, Yuko; Egawa, Takahiro; Kamiya, Mako; Komatsu, Toru; Ueno, Tasuku; Terai, Takuya; Yoshida, Kengo; Uchiyama, Masanobu; Nagano, Tetsuo; Urano, Yasuteru

2015-09-01

Fluorescein is a representative green fluorophore that has been widely used as a scaffold of practically useful green fluorescent probes. Here, we report synthesis and characterization of a silicon-substituted fluorescein, i.e., 2-COOH TokyoMagenta (2-COOH TM), which is a fluorescein analogue in which the O atom at the 10' position of the xanthene moiety of fluorescein is replaced with a Si atom. This fluorescein analogue forms a spirolactone ring via intramolecular nucleophilic attack of the carboxylic group in a pH-dependent manner. Consequently, 2-COOH TM exhibits characteristic large pH-dependent absorption and fluorescence spectral changes: (1) 2-COOH TM is colorless at acidic pH, whereas fluorescein retains observable absorption and fluorescence even at acidic pH, and the absorption maximum is also shifted; (2) the absorption spectral change occurs above pH 7.0 for 2-COOH TM and below pH 7.0 for fluorescein; (3) 2-COOH TM shows a much sharper pH response than fluorescein because of its pKa inversion, i.e., pKa1 > pKa2. These features are also different from those of a compound without the carboxylic group, 2-Me TokyoMagenta (2-Me TM). Analysis of the chemical equilibrium between pH 3.0 and 11.0 disclosed that 2-COOH TM favors the colorless and nonfluorescent lactone form, compared with fluorescein. Substitution of Cl atoms at the 4' and 5' positions of the xanthene moiety of 2-COOH TM to obtain 2-COOH DCTM shifted the equilibrium so that the new derivative exists predominantly in the strongly fluorescent open form at physiological pH (pH 7.4). To demonstrate the practical utility of 2-COOH DCTM as a novel scaffold for red fluorescent probes, we employed it to develop a probe for β-galactosidase.

Graft protective effect and induction of CD4+Foxp3+ cell by Thrombomodulin on allograft arteriosclerosis in mice.

PubMed

Yin, Enzhi; Matsuyama, Shigefumi; Uchiyama, Masateru; Kawai, Kento; Niimi, Masanori

2018-05-21

Thrombomodulin (TM) is a promising therapeutic natural anti-coagulant, which exerts the effects to control disseminated intravascular coagulation. However, little is known whether TM on micro-vessels could play an important role in the regulation of intimal hyperplasia. We investigated the vessel-protective effect of TM in the survival of fully major histocompatibility complex (MHC)-mismatched murine cardiac allograft transplantation. CBA recipients transplanted with a C57BL/6 heart received intraperitoneal administration of normal saline or 0.2, 2.0, and 20.0 μg/day of TM for 7 days (n = 5, 7, 11, and 11, respectively). Immunohistochemical and fluorescent staining studies were performed to determine whether CD4 + Foxp3 + regulatory T cell were generated at 2 and 4 weeks after grafting. Morphometric analysis for neointimal formation in the coronary arteries of the transplanted allograft was conducted at 2 and 4 weeks after grafting. Untreated CBA recipients rejected C57BL/6 cardiac grafts acutely (median survival time [MST], 7 days). CBA recipients exposed with the above doses had significantly prolonged allograft survival (MSTs, 17, 24 and 50 days, respectively). Morphometric assessment showed that intimal hyperplasia was clearly suppressed in the left and right coronary arteries or allografts from TM-exposed recipients 2 and 4 weeks. Immunohistochemical studies at 2 weeks showed more CD4 + Foxp3 + cells and lower myocardial damage in the allografts from TM-exposed recipients. Notably, fluorescent staining studies demonstrated that TM-exposed recipients 4 weeks post-engraftment had strong aggregation of CD4 + Foxp3 + cells in the intima of the coronary arteries of the cardiac allografts. TM may prolong the survival of fully MHC-mismatched cardiac allografts through suppressing intimal hyperplasia and inducing the accumulation of regulatory CD4 + Foxp3 + cells within coronary arteries.

Electronic and magnetic properties of transition metal doped graphyne

NASA Astrophysics Data System (ADS)

Gangan, Abhijeet Sadashiv; Yadav, Asha S.; Chakraborty, Brahmananda; Ramaniah, Lavanya M.

2017-05-01

We have theoretically investigated the interaction of few 3d (V,Mn) and 4d (Y,Zr) transition metals with the γ-graphyne structure using the spin-polarized density functional theory for its potentials application in Hydrogen storage, spintronics and nano-electronics. By doping different TMs we have observed that the system can be either metallic(Y), semi-conducting or half metallic. The system for Y and Zr doped graphyne becomes non-magnetic while V and Mn doped graphyne have a magnetic moments of l μB and 3 μB respectively From bader charge analysis it is seen that there is a charge transfer from the TM atom to the graphyne. Zr and Y have a net charge transfer of 2.15e and 1.73e respectively. Charge density analysis also shows the polarization on the carbon skeleton which becomes larger as the charge transfer for the TM atom increases. Thus we see Y and Zr are better candidates for hydrogen storage devices since they are non-magnetic and have less d electrons which is ideal for kubas-type interactions between hydrogen molecule and TM.

Long-Term Storage at -80°C: Effect on Rate of Recovery of Mycobacterium tuberculosis From Direct Acid-Fast Bacilli Smear-Positive Sputum Samples.

PubMed

Shinu, Pottathil; AshokKumar Singh, Varsha; Nair, Anroop; Farooq, Rumana; Ishaq, Sheikh

2016-09-01

The aim of this study was to evaluate the difference in the rate of recovery of Mycobacterium tuberculosis (MTB) from routinely cultured sputum and long-term stored sputum specimens (at -80°C) using Löwenstein-Jensen (LJ) media, Mycobacterium Growth Indicator Tube (BBL MGIT(TM) ), and Middlebrook 7H11 (MB 7H11) agar. Direct acid-fast bacilli smear-positive sputum specimens (both before and after storage [n = 136]) were studied (after culturing on LJ media, BBL MGIT(TM) , and MB 7H11 agar) and the performances were compared. For the detection of MTB, BBL MGIT(TM) and MB 7H11 agar (before storage) demonstrated a sensitivity, specificity, positive predictive value (PPV) of 98.28%, 30.77%, 92.68%, 66.67%, and negative predictive value (NPV) of 97.41%, 30.77%, 92.62%, 57.14%, respectively, when compared to LJ media (before storage). Similarly, BBL MGIT(TM) and MB 7H11 agar (after storage) demonstrated a sensitivity, specificity, PPV, and NPV of 95.5%, 38.89%, 90.6%, 58.33%, and 95.5%, 66.67 %, 94.64%, 70.59%, respectively, when compared to LJ media (after storage) for the detection of MTB. None of the culture techniques independently (both before and after storage) detected growth of MTB from all the sputum specimens studied. However, BBL MGIT(TM) system and LJ media combination (both before and after storage) effectively detected the growth of MTB from sputum specimens when compared to other culture technique combinations. © 2015 Wiley Periodicals, Inc.

Bimolecular fluorescence complementation: lighting up seven transmembrane domain receptor signalling networks

PubMed Central

Rose, Rachel H; Briddon, Stephen J; Holliday, Nicholas D

2010-01-01

There is increasing complexity in the organization of seven transmembrane domain (7TM) receptor signalling pathways, and in the ability of their ligands to modulate and direct this signalling. Underlying these events is a network of protein interactions between the 7TM receptors themselves and associated effectors, such as G proteins and β-arrestins. Bimolecular fluorescence complementation, or BiFC, is a technique capable of detecting these protein–protein events essential for 7TM receptor function. Fluorescent proteins, such as those from Aequorea victoria, are split into two non-fluorescent halves, which then tag the proteins under study. On association, these fragments refold and regenerate a mature fluorescent protein, producing a BiFC signal indicative of complex formation. Here, we review the experimental criteria for successful application of BiFC, considered in the context of 7TM receptor signalling events such as receptor dimerization, G protein and β-arrestin signalling. The advantages and limitations of BiFC imaging are compared with alternative resonance energy transfer techniques. We show that the essential simplicity of the fluorescent BiFC measurement allows high-content and advanced imaging applications, and that it can probe more complex multi-protein interactions alone or in combination with resonance energy transfer. These capabilities suggest that BiFC techniques will become ever more useful in the analysis of ligand and 7TM receptor pharmacology at the molecular level of protein–protein interactions. This article is part of a themed section on Imaging in Pharmacology. To view the editorial for this themed section visit http://dx.doi.org/10.1111/j.1476-5381.2010.00685.x PMID:20015298

Ligand Entry and Exit Pathways in the β2-adrenergic Receptor

PubMed Central

Wang, Ting; Duan, Yong

2009-01-01

The recently determined crystal structure of the human β2-adrenergic (β2AR) G-protein coupled receptor provides an excellent structural basis for exploring β2AR -ligand binding and dissociation process. Based on this crystal structure, we simulated ligand exit from the β2AR receptor by applying the random acceleration molecular dynamics (RAMD) simulation method. The simulation results showed that the extracellular opening on the receptor surface was the most frequently observed egress point (referred to as pathway A) and a few other pathways through inter-helical clefts were also observed with significantly lower frequencies. In the egress trajectories along pathway A, the D192-K305 salt bridge between the extracellular loop 2 (ECL2) and the apex of the transmembrane helix 7 (TM7) was exclusively broken. The spatial occupancy maps of the ligand computed from the 100 RAMD simulation trajectories indicated that the receptor-ligand interactions that restrained the ligand in the binding pocket were the major resistance encountered by the ligand during exit and no second barrier was notable. We next performed RAMD simulations by using a putative ligand-free conformation of the receptor as input structure. This conformation was obtained in a standard MD simulation in the absence of the ligand and it differed from the ligand-bound conformation in a hydrophobic patch bridging ECL2 and TM7 due to the rotation of F193 of ECL2. Results from the RAMD simulations with this putative ligand-free conformation suggest that the cleft formed by the hydrophobic bridge, TM2, TM3 and TM7 on the extracellular surface likely serves as a more specific ligand-entry site and the ECL2-TM7 hydrophobic junction can be partially interrupted upon the entry of ligand that pushes F193 to rotate, resulting in a conformation as observed in the ligand-bound crystal structure. These results may help design β2AR-targeting drugs with improved efficacy as well as understand the receptor subtype-selectivity of ligand binding in the β family of the adrenergic receptors that share almost identical ligand-binding pockets but show notable amino acid sequence divergence in the putative ligand-entry site, including ECL2 and the extracellular end of TM7. PMID:19665031

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

Faham, S.; Watanabe, A.; Besserer, G.M.

Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The -3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of themore » leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.« less

Determining successional stage of temperate coniferous forests with Landsat satellite data

NASA Technical Reports Server (NTRS)

Fiorella, Maria; Ripple, William J.

1995-01-01

Thematic Mapper (TM) digital imagery was used to map forest successional stages and to evaluate spectral differences between old-growth and mature forests in the central Cascade Range of Oregon. Relative sun incidence values were incorporated into the successional stage classification to compensate for topographic induced variation. Relative sun incidence improved the classification accuracy of young successional stages, but did not improve the classification accuracy of older, closed canopy forest classes or overall accuracy. TM bands 1, 2, and 4; the normalized difference vegetation index (NDVI); and TM 4/3, 4/5, and 4/7 band ratio values for old-growth forests were found to be significantly lower than the values of mature forests (P less than or equal to 0.010). Wetness and the TM 4/5 and 4/7 band ratios all had low correlations to relative sun incidence (r(exp 2) less than or equal to 0.16). The TM 4/5 band ratio was named the 'structural index' (SI) because of its ability to distinguish between mature and old-growth forests and its simplicity.

Lattice sites of ion-implanted Mn, Fe and Ni in 6H-SiC

NASA Astrophysics Data System (ADS)

Costa, A. R. G.; Wahl, U.; Correia, J. G.; David-Bosne, E.; Amorim, L. M.; Augustyns, V.; Silva, D. J.; da Silva, M. R.; Pereira, L. M. C.

2018-01-01

Using radioactive isotopes produced at the CERN-ISOLDE facility, the lattice location of the implanted transition metal (TM) ions 56Mn, 59Fe and 65Ni in n-type single-crystalline hexagonal 6H-SiC was studied by means of the emission channeling technique. TM probes on carbon coordinated tetrahedral interstitial sites (T C) and on substitutional silicon sites (S Si,h+k ) were identified. We tested for but found no indication that the TM distribution on S Si sites deviates from the statistical mixture of 1/3 hexagonal and 2/3 cubic sites present in the 6H crystal. The TM atoms partially disappear from T C positions during annealing at temperatures between 500 °C and 700 °C which is accompanied by an increase on S Si and random sites. From the temperature associated with these site changes, interstitial migration energies of 1.7-2.7 eV for Mn and Ni, and 2.3-3.2 eV for Fe were estimated. TM lattice locations are compared to previous results obtained in 3C-SiC using the same technique.

Giving the early fossil record of sponges a squeeze.

PubMed

Antcliffe, Jonathan B; Callow, Richard H T; Brasier, Martin D

2014-11-01

Twenty candidate fossils with claim to be the oldest representative of the Phylum Porifera have been re-analysed. Three criteria are used to assess each candidate: (i) the diagnostic criteria needed to categorize sponges in the fossil record; (ii) the presence, or absence, of such diagnostic features in the putative poriferan fossils; and (iii) the age constraints for the candidate fossils. All three criteria are critical to the correct interpretation of any fossil and its placement within an evolutionary context. Our analysis shows that no Precambrian fossil candidate yet satisfies all three of these criteria to be a reliable sponge fossil. The oldest widely accepted candidate, Mongolian silica hexacts from c. 545 million years ago (Ma), are here shown to be cruciform arsenopyrite crystals. The oldest reliable sponge remains are siliceous spicules from the basal Cambrian (Protohertzina anabarica Zone) Soltanieh Formation, Iran, which are described and analysed here in detail for the first time. Extensive archaeocyathan sponge reefs emerge and radiate as late as the middle of the Fortunian Stage of the Cambrian and demonstrate a gradual assembly of their skeletal structure through this time coincident with the evolution of other metazoan groups. Since the Porifera are basal in the Metazoa, their presence within the late Proterozoic has been widely anticipated. Molecular clock calibration for the earliest Porifera and Metazoa should now be based on the Iranian hexactinellid material dated to c. 535 Ma. The earliest convincing fossil sponge remains appeared at around the time of the Precambrian-Cambrian boundary, associated with the great radiation events of that interval. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Modeling and Decision Support Tools Based on the Effects to Sediment Geochemistry and Microbial Populations on Contaminant Reactions in Sediments

DTIC Science & Technology

2011-09-01

Deltaproteobacteria(4) Others(5) Unclassified bacteria(7) Nitrospira(2) Actinobacteria (2) Betaproteobacteria(17) Re su lts  a nd  D is cu...3/7.18E-1) » » » phylum Actinobacteria (2/0/2.38E-1) » » » » class Actinobacteria (2/0/2.38E-1) » » » » » subclass Coriobacteridae

Study on the Immunoreactivity of Triticum monococcum (Einkorn) Wheat in Patients with Wheat-Dependent Exercise-Induced Anaphylaxis for the Production of Hypoallergenic Foods.

PubMed

Lombardo, Carla; Bolla, Michela; Chignola, Roberto; Senna, Gianenrico; Rossin, Giacomo; Caruso, Beatrice; Tomelleri, Carlo; Cecconi, Daniela; Brandolini, Andrea; Zoccatelli, Gianni

2015-09-23

Wheat [Triticum aestivum (T.a.)] ingestion can cause a specific allergic reaction, which is called wheat-dependent exercise-induced anaphylaxis (WDEIA). The major allergen involved is ω-5 gliadin, a gluten protein coded by genes located on the B genome. Our aim was to study the immunoreactivity of proteins in Triticum monococcum (einkorn, T.m.), a diploid ancestral wheat lacking B chromosomes, for possible use in the production of hypoallergenic foods. A total of 14 patients with a clear history of WDEIA and specific immunoglobulin E (IgE) to ω-5 gliadin were enrolled. Skin prick test (SPT) with a commercial wheat extract and an in-house T.a. gluten diagnostic solution tested positive for 43 and 100% of the cases, respectively. No reactivity in patients tested with solutions prepared from four T.m. accessions was observed. The immunoblotting of T.m. gluten proteins performed with the sera of patients showed different IgE-binding profiles with respect to T.a., confirming the absence of ω-5 gliadin. A general lower immunoreactivity of T.m. gluten proteins with scarce cross-reactivity to ω-5 gliadin epitopes was assessed by an enzyme-linked immunosorbent assay (ELISA). Given the absence of reactivity by SPT and the limited cross-reactivity with ω-5 gliadin, T.m. might represent a potential candidate in the production of hypoallergenic bakery products for patients sensitized to ω-5 gliadin. Further analyses need to be carried out regarding its safety.

Assessment of Thematic Mapper band-to-band registration by the block correlation method

NASA Technical Reports Server (NTRS)

Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

1983-01-01

Rectangular blocks of pixels from one band image were statistically correlated against blocks centered on identical pixels from a second band image. The block pairs were shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient to the maximum correlation was taken as the best estimate of registration error for each block pair. For the band combinations of the Arkansas scene studied, the misregistration of TM spectral bands within the noncooled focal plane lie well within the 0.2 pixel target specification. Misregistration between the middle IR bands is well within this specification also. The thermal IR band has an apparent misregistration with TM band 7 of approximately 3 pixels in each direction. The TM band 3 has a misregistration of approximately 0.2 pixel in the across-scan direction and 0.5 pixel in the along-scan direction, with both TM bands 5 and 7.

Assessment of Thematic Mapper Band-to-band Registration by the Block Correlation Method

NASA Technical Reports Server (NTRS)

Card, D. H.; Wrigley, R. C.; Mertz, F. C.; Hall, J. R.

1985-01-01

Rectangular blocks of pixels from one band image were statistically correlated against blocks centered on identical pixels from a second band image. The block pairs were shifted in pixel increments both vertically and horizontally with respect to each other and the correlation coefficient to the maximum correlation was taken as the best estimate of registration error for each block pair. For the band combinations of the Arkansas scene studied, the misregistration of TM spectral bands within the noncooled focal plane lie well within the 0.2 pixel target specification. Misregistration between the middle IR bands is well within this specification also. The thermal IR band has an apparent misregistration with TM band 7 of approximately 3 pixels in each direction. The TM band 3 has a misregistration of approximately 0.2 pixel in the across-scan direction and 0.5 pixel in the along-scan direction, with both TM bands 5 and 7.

LANDSAT-4 image data quality analysis for energy related applications. [nuclear power plant sites

NASA Technical Reports Server (NTRS)

Wukelic, G. E. (Principal Investigator)

1983-01-01

No useable LANDSAT 4 TM data were obtained for the Hanford site in the Columbia Plateau region, but TM simulator data for a Virginia Electric Company nuclear power plant was used to test image processing algorithms. Principal component analyses of this data set clearly indicated that thermal plumes in surface waters used for reactor cooling would be discrenible. Image processing and analysis programs were successfully testing using the 7 band Arkansas test scene and preliminary analysis of TM data for the Savanah River Plant shows that current interactive, image enhancement, analysis and integration techniques can be effectively used for LANDSAT 4 data. Thermal band data appear adequate for gross estimates of thermal changes occurring near operating nuclear facilities especially in surface water bodies being used for reactor cooling purposes. Additional image processing software was written and tested which provides for more rapid and effective analysis of the 7 band TM data.

Lowered pH Alters Decay but Not Speed of Tectorial Membrane Waves

NASA Astrophysics Data System (ADS)

Farrahi, Shirin; Ghaffari, Roozbeh; Freeman, Dennis M.

2011-11-01

Tectorial membrane (TM) traveling waves and mechanical shear impedances were measured in artificial endolymph baths at neutral and acidic pHs. Lowering pH from 7 to 4 significantly decreases the spatial extent of TM waves but has a relatively minor effect on wave speed. At pH 4, the imaginary component of TM shear impedance, which relates to the shear modulus, drops significantly; whereas, the real component, which relates to viscosity, is reduced less. These results suggest that shear modulus, and not viscosity, controls the extent of TM waves at lower pH.

Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

PubMed

Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

2015-12-01

The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A transducer for microbial sensory rhodopsin that adopts GTG as a start codon is identified in Haloarcula marismortui.

PubMed

Fu, Hsu-Yuan; Lu, Yen-Hsu; Yi, Hsiu-Ping; Yang, Chii-Shen

2013-04-05

Microbial sensory rhodopsins are known to mediate phototaxis, and all of the known sensory rhodopsins execute this function with a specific cognate transducer that has two-transmembrane (2-TM) regions. In the genome of Haloarcula marismortui, a total of six rhodopsin genes were annotated, and we previously showed three of them to be the ion type and suggested the other three as sensory type, even though the candidate transducer gene, htr, for HmSRI was missing the 2-TM region that is found in all of the other known transducers. Here we showed this htr gene featured a preceding 2-TM region when the alternative start codon GTG located 291 nucleotides upstream of the original annotated open reading frame (ORF) was introduced and it is named as htrI in this study. Overexpression of HmHtrI exhibited it existed as a membrane protein and several biophysical assays confirmed it functionally interacted with HmSRI. Together with our previous reverse-transcriptase-PCR results and phototaxis measurements, the new ORF of original predicted soluble htr gene product was a membrane protein with a 2-TM region, HmHtrI; and it serves as the cognate transducer for HmSRI. HmHtrI therefore is the first transducer for the sensory rhodopsin adopted start codon other than ATG. Copyright © 2013 Elsevier B.V. All rights reserved.

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

PubMed Central

Fujio-Vejar, Sayaka; Vasquez, Yessenia; Morales, Pamela; Magne, Fabien; Vera-Wolf, Patricia; Ugalde, Juan A.; Navarrete, Paola; Gotteland, Martin

2017-01-01

The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing. Fecal samples were collected from 41 young, asymptomatic, normal weight volunteers (age: 25 ± 4 years; ♀:48.8%; BMI: 22.5 ± 1.6 kg/m2) with low levels of plasma (IL6 and hsCRP) and colonic (fecal calprotectin) inflammatory markers. The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system. 109,180 ± 13,148 sequences/sample were obtained, with an α-diversity of 3.86 ± 0.37. The dominant phyla were Firmicutes (43.6 ± 9.2%) and Bacteroidetes (41.6 ± 13.1%), followed by Verrucomicrobia (8.5 ± 10.4%), Proteobacteria (2.8 ± 4.8%), Actinobacteria (1.8 ± 3.9%) and Euryarchaeota (1.4 ± 2.7%). The core microbiota representing the genera present in all the subjects included Bacteroides, Prevotella, Parabacteroides (phylum Bacteroidetes), Phascolarctobacterium, Faecalibacterium, Ruminococcus, Lachnospira, Oscillospira, Blautia, Dorea, Roseburia, Coprococcus, Clostridium, Streptococcus (phylum Firmicutes), Akkermansia (phylum Verrucomicrobia), and Collinsella (phylum Actinobacteria). Butyrate-producing genera including Faecalibacterium, Roseburia, Coprococcus, and Oscillospira were detected. The family Methanobacteriaceae was reported in 83% of the subjects and Desulfovibrio, the most representative sulfate-reducing genus, in 76%. The microbiota of the Chilean individuals significantly differed from those of Papua New Guinea and the Matses ethnic group and was closer to that of the Argentinians and sub-populations from the United States. Interestingly, the microbiota of the Chilean subjects stands out for its richness in Verrucomicrobia; the mucus-degrading bacterium Akkermansia muciniphila is the only identified member of this phylum. This is an important finding considering that this microorganism has been recently proposed as a hallmark of healthy gut due to its anti-inflammatory and immunostimulant properties and its ability to improve gut barrier function, insulin sensitivity and endotoxinemia. These results constitute an important baseline that will facilitate the characterization of dysbiosis in the main diseases affecting the Chilean population. PMID:28713349

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia.

PubMed

Fujio-Vejar, Sayaka; Vasquez, Yessenia; Morales, Pamela; Magne, Fabien; Vera-Wolf, Patricia; Ugalde, Juan A; Navarrete, Paola; Gotteland, Martin

2017-01-01

The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing. Fecal samples were collected from 41 young, asymptomatic, normal weight volunteers (age: 25 ± 4 years; ♀:48.8%; BMI: 22.5 ± 1.6 kg/m 2 ) with low levels of plasma (IL6 and hsCRP) and colonic (fecal calprotectin) inflammatory markers. The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system. 109,180 ± 13,148 sequences/sample were obtained, with an α-diversity of 3.86 ± 0.37. The dominant phyla were Firmicutes (43.6 ± 9.2%) and Bacteroidetes (41.6 ± 13.1%), followed by Verrucomicrobia (8.5 ± 10.4%), Proteobacteria (2.8 ± 4.8%), Actinobacteria (1.8 ± 3.9%) and Euryarchaeota (1.4 ± 2.7%). The core microbiota representing the genera present in all the subjects included Bacteroides , Prevotella , Parabacteroides (phylum Bacteroidetes), Phascolarctobacterium , Faecalibacterium , Ruminococcus , Lachnospira , Oscillospira , Blautia , Dorea , Roseburia , Coprococcus , Clostridium , Streptococcus (phylum Firmicutes), Akkermansia (phylum Verrucomicrobia), and Collinsella (phylum Actinobacteria). Butyrate-producing genera including Faecalibacterium , Roseburia , Coprococcus , and Oscillospira were detected. The family Methanobacteriaceae was reported in 83% of the subjects and Desulfovibrio , the most representative sulfate-reducing genus, in 76%. The microbiota of the Chilean individuals significantly differed from those of Papua New Guinea and the Matses ethnic group and was closer to that of the Argentinians and sub-populations from the United States. Interestingly, the microbiota of the Chilean subjects stands out for its richness in Verrucomicrobia; the mucus-degrading bacterium Akkermansia muciniphila is the only identified member of this phylum. This is an important finding considering that this microorganism has been recently proposed as a hallmark of healthy gut due to its anti-inflammatory and immunostimulant properties and its ability to improve gut barrier function, insulin sensitivity and endotoxinemia. These results constitute an important baseline that will facilitate the characterization of dysbiosis in the main diseases affecting the Chilean population.

Mapping chromatic pathways in the Drosophila visual system.

PubMed

Lin, Tzu-Yang; Luo, Jiangnan; Shinomiya, Kazunori; Ting, Chun-Yuan; Lu, Zhiyuan; Meinertzhagen, Ian A; Lee, Chi-Hon

2016-02-01

In Drosophila, color vision and wavelength-selective behaviors are mediated by the compound eye's narrow-spectrum photoreceptors R7 and R8 and their downstream medulla projection (Tm) neurons Tm5a, Tm5b, Tm5c, and Tm20 in the second optic neuropil or medulla. These chromatic Tm neurons project axons to a deeper optic neuropil, the lobula, which in insects has been implicated in processing and relaying color information to the central brain. The synaptic targets of the chromatic Tm neurons in the lobula are not known, however. Using a modified GFP reconstitution across synaptic partners (GRASP) method to probe connections between the chromatic Tm neurons and 28 known and novel types of lobula neurons, we identify anatomically the visual projection neurons LT11 and LC14 and the lobula intrinsic neurons Li3 and Li4 as synaptic targets of the chromatic Tm neurons. Single-cell GRASP analyses reveal that Li4 receives synaptic contacts from over 90% of all four types of chromatic Tm neurons, whereas LT11 is postsynaptic to the chromatic Tm neurons, with only modest selectivity and at a lower frequency and density. To visualize synaptic contacts at the ultrastructural level, we develop and apply a "two-tag" double-labeling method to label LT11's dendrites and the mitochondria in Tm5c's presynaptic terminals. Serial electron microscopic reconstruction confirms that LT11 receives direct contacts from Tm5c. This method would be generally applicable to map the connections of large complex neurons in Drosophila and other animals. © 2015 Wiley Periodicals, Inc.

Revisiting Metchnikoff: Age-related alterations in microbiota-gut-brain axis in the mouse.

PubMed

Scott, Karen A; Ida, Masayuki; Peterson, Veronica L; Prenderville, Jack A; Moloney, Gerard M; Izumo, Takayuki; Murphy, Kiera; Murphy, Amy; Ross, R Paul; Stanton, Catherine; Dinan, Timothy G; Cryan, John F

2017-10-01

Over the last decade, there has been increased interest in the role of the gut microbiome in health including brain health. This is by no means a new theory; Elie Metchnikoff proposed over a century ago that targeting the gut by consuming lactic acid bacteria such as those in yogurt, could improve or delay the onset of cognitive decline associated with ageing. However, there is limited information characterising the relationship between the behavioural and physiological sequelae of ageing and alterations in the gut microbiome. To this end, we assessed the behavioural, physiological and caecal microbiota profile of aged male mice. Older mice (20-21months old) exhibited deficits in spatial memory and increases in anxiety-like behaviours compared to younger mice (2-3months old). They also exhibited increased gut permeability, which was directly correlated with elevations in peripheral pro-inflammatory cytokines. Furthermore, stress exacerbated the gut permeability of aged mice. Examination of the caecal microbiota revealed significant increases in phylum TM7, family Porphyromonadaceae and genus Odoribacter of aged mice. This represents a shift of aged microbiota towards a profile previously associated with inflammatory disease, particularly gastrointestinal and liver disorders. Furthermore, Porphyromonadaceae, which has also been associated with cognitive decline and affective disorders, was directly correlated with anxiety-like behaviour in aged mice. These changes suggest that changes in the gut microbiota and associated increases in gut permeability and peripheral inflammation may be important mediators of the impairments in behavioural, affective and cognitive functions seen in ageing. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential Diagnosis in Idiopathic Granulomatous Mastitis and Tuberculous Mastitis

PubMed Central

Seo, Hee Ri Na; Na, Kuk Young; Yim, Hyun Ee; Kim, Tae Hee; Kang, Doo Kyoung; Oh, Ki Keun; Kang, Seok Yun; An, Young-Sil; Chun, Mison; Kim, Woojae; Park, Rae Woong; Jung, Yong Sik

2012-01-01

Purpose Idiopathic granulomatous mastitis (IGM) is a rare chronic inflammatory disease of unknown etiology. The diagnosis of IGM requires that other granulomatous lesions in the breast be excluded. Tuberculous mastitis (TM) is also an uncommon disease that is often difficult to differentiate from IGM. The purpose of this study is to develop a new algorithm for the differential diagnosis and treatment of IGM and TM. Methods Medical records of 68 patients (58 with IGM and 10 with TM) between July 1999 and February 2009 were retrospectively reviewed. Results The mean age of the patients was 33.5 (IGM) and 40 (TM) years (p=0.018). The median follow-up was 84 months. Of the total 10 patients with TM, 5 patients had a history of pulmonary tuberculosis. The most common symptoms of the diseases were breast lump and pain. However, axillary lymphadenopathy was more seen in TM (50%) compared to IGM (20.6%) (p=0.048). TM showed more cancer-mimicking findings on radiologic study (p=0.028). In IGM, 48 patients (82.7%) underwent surgical wide excision and 21 patients (36.2%) were managed with corticosteroid therapy and antibiotics. All of the TM patients received anti-tuberculosis medications and 9 patients (90%) underwent wide excision. The mean treatment duration was 2.8 months in IGM and 8.4 months in TM. Recurrence developed in 5 patients (8.6%) in IGM and 1 patient (10%) in TM. Conclusion This study shows different characteristics between IGM and TM. The IGM patients were younger and had more mastalgia symptoms than the TM patients. Axillary lymphadenopathy was seen more often in TM patients. Half of the TM patients had pulmonary tuberculosis or tuberculosis lymphadenitis. Surgical wide excision might be both therapeutic and useful for providing an exact diagnosis. PMID:22493637

Effect of silica surface coating on the luminescence lifetime and upconversion temperature sensing properties of semiconductor zinc oxide doped with gallium(III) and sensitized with rare earth ions Yb(III) and Tm(III).

PubMed

Li, Yuemei; Li, Yongmei; Wang, Rui; Zheng, Wei

2018-02-26

Optical sensing of temperature by measurement of the ratio of the intensities of the 700 nm emission and the 800 nm emission of Ga(III)-doped ZnO (GZO) nanoparticles (NPs) and of GZO NPs coated with a silica shell are demonstrated at 980 nm excitation. It is found that the relative sensitivity of SiO 2 @Yb/Tm/GZO is 6.2% K -1 at a temperature of 693 K. This is ~3.4 times higher than that of Yb/Tm/GZO NPs. Obviously, the SiO 2 shell structure decreases the rate of the nonradiative decay. The decay time of the 800 nm emission of the Yb/Tm/GZO NPs (15 mol% Ga; 7 mol% Yb; 0.5 mol% Tm) displays a biexponential decay with a dominant decay time of 148 μs and a second decay time of ~412 μs. The lifetime of the Yb/Tm/GZO NPs at 293 K, and of the SiO 2 @Yb/Tm/GZO NPs are ~412 μs. Both the Yb/Tm/GZO and SiO 2 @Yb/Tm/GZO can be used up to 693 K. These results indicate that the SiO 2 shell on the Yb/Tm/GZO is beneficial in terms of sensitivity and resolution. Graphical abstract The enhancement the decay time and thermal sensitivity in the SiO 2 @Yb/Tm/GZO shell@core structure have been studied compared to the Ga(III)-doped Yb/Tm-doped ZnO (Yb/Tm/GZO). The SiO 2 @Yb/Tm/GZO have good thermal accuracy up to 693 °C.

Two Different Conformations in Hepatitis C Virus p7 Protein Account for Proton Transport and Dye Release

PubMed Central

Vararattanavech, Ardcharaporn; Torres, Jaume

2014-01-01

The p7 protein from the hepatitis C virus (HCV) is a 63 amino acid long polypeptide that is essential for replication, and is involved in protein trafficking and proton transport. Therefore, p7 is a possible target for antivirals. The consensus model for the channel formed by p7 protein is a hexameric or heptameric oligomer of α-helical hairpin monomers, each having two transmembrane domains, TM1 and TM2, where the N-terminal TM1 would face the lumen of this channel. A reported high-throughput functional assay to search for p7 channel inhibitors is based on carboxyfluorescein (CF) release from liposomes after p7 addition. However, the rationale for the dual ability of p7 to serve as an ion or proton channel in the infected cell, and to permeabilize membranes to large molecules like CF is not clear. We have recreated both activities in vitro, examining the conformation present in these assays using infrared spectroscopy. Our results indicate that an α-helical form of p7, which can transport protons, is not able to elicit CF release. In contrast, membrane permeabilization to CF is observed when p7 contains a high percentage of β-structure, or when using a C-terminal fragment of p7, encompassing TM2. We propose that the reported inhibitory effect of some small compounds, e.g., rimantadine, on both CF release and proton transport can be explained via binding to the membrane-inserted C-terminal half of p7, increasing its rigidity, in a similar way to the influenza A M2-rimantadine interaction. PMID:24409277

TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content

PubMed Central

Mahdessian, Hovsep; Taxiarchis, Apostolos; Popov, Sergej; Silveira, Angela; Franco-Cereceda, Anders; Hamsten, Anders; Eriksson, Per; van't Hooft, Ferdinand

2014-01-01

Genome-wide association studies have identified a locus on chromosome 19 associated with plasma triglyceride (TG) concentration and nonalcoholic fatty liver disease. However, the identity and functional role of the gene(s) responsible for these associations remain unknown. Of 19 expressed genes contained in this locus, none has previously been implicated in lipid metabolism. We performed gene expression studies and expression quantitative trait locus analysis in 206 human liver samples to identify the putative causal gene. Transmembrane 6 superfamily member 2 (TM6SF2), a gene with hitherto unknown function, expressed predominantly in liver and intestine, was identified as the putative causal gene. TM6SF2 encodes a protein of 351 amino acids with 7–10 predicted transmembrane domains. Otherwise, no other protein features were identified which could help to elucidate the function of TM6SF2. Protein subcellular localization studies with confocal microscopy demonstrated that TM6SF2 is localized in the endoplasmic reticulum and the ER-Golgi intermediate compartment of human liver cells. Functional studies for secretion of TG-rich lipoproteins (TRLs) and lipid droplet content were performed in human hepatoma Huh7 and HepG2 cells using confocal microscopy and siRNA inhibition and overexpression techniques. In agreement with the genome-wide association data, it was found that TM6SF2 siRNA inhibition was associated with reduced secretion of TRLs and increased cellular TG concentration and lipid droplet content, whereas TM6SF2 overexpression reduced liver cell steatosis. We conclude that TM6SF2 is a regulator of liver fat metabolism with opposing effects on the secretion of TRLs and hepatic lipid droplet content. PMID:24927523

Metabolic responses associated with deer hunting.

PubMed

Peterson, A T; Steffen, J; Terry, L; Davis, J; Porcari, J P; Foster, C

1999-12-01

Deer hunting is a popular recreational activity with a high rate of cardiovascular events. Previous studies have demonstrated large HR responses during deer hunting. This study compared the HR and metabolic costs of maximal treadmill (TM) exercise with those of hiking while deer hunting and while dragging a deer. Healthy male volunteers (N = 16) performed a maximal TM exercise test, a 0.8-km hiking test, and a 0.4-km dragging test over lightly rolling terrain. VO2 was measured by portable spirometry and HR by radiotelemetry. HR averaged 74.0 +/- 7.0% and 89.1 +/- 4.5% of peak TM HR during the hike and drag, respectively. The peak HR observed during hiking and dragging was 83.2 +/- 6.0% and 94.9 +/- 4.2% of peak TM HR, respectively. VO2 averaged 62.2 +/- 15.8% and achieved a peak of 77.2 +/- 19.0% of TM VO2 while hiking. This corresponded to 86.8 +/- 17.3% and 108.1 +/- 22.3% of ventilatory threshold (VT), respectively. VO2 averaged 72.3 +/- 21.0% and achieved a peak of 91.2 +/- 21.4% of peak TM VO2 while dragging the deer. This corresponded to 101.5 +/- 27.7% and 128.5 +/- 26.8% of VT, respectively. The VO2/HR relationship showed significant (P < 0.05) difference between the dragging test and the TM test with a disproportionately high HR. The VO2/HR relationship between the hiking and TM tests was comparable. In part, the previously described large HR responses and high rate of cardiovascular complications associated with deer hunting may attributable to the elevated metabolic costs of associated activities.

Tuning the Hydrogen Storage in Magnesium Alloys

NASA Astrophysics Data System (ADS)

Er, Suleyman; de Wijs, Gilles A.; Brocks, Geert

2011-03-01

We investigate the hydrogen storage properties of promising magnesium alloys. Mg H2 (7.6 wt % H) would be a very useful storage material if the (de)hydrogenation kinetics can be improved and the desorption temperature is markedly lowered. Using first principles calculations, we show that hydrides of Mg-transition metal (TM) alloys adopt a structure that promotes faster (de)hydrogenation kinetics, as is also observed in experiment. Within the lightweight TMs, the most promising alloying element is titanium. Alloying Mg with Ti alone, however, is not sufficient to decrease the stability of the hydride phases, which is necessary to reduce the hydrogen desorption temperature. We find that adding aluminium or silicon markedly destabilizes Mg-Ti hydrides and stabilizes Mg-Ti alloys. Finally, we show that controlling the structure of Mg-Ti-Al(Si) system by growing it as multilayers, has a beneficial influence on the thermodynamic properties and makes it a stronger candidate for hydrogen storage.

Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.

PubMed

Zeng, Yin-Xin; Yan, Ming; Yu, Yong; Li, Hui-Rong; He, Jian-Feng; Sun, Kun; Zhang, Fang

2013-05-01

Two 16S rRNA gene clone libraries Cores 1U and 2U were constructed using two ice core samples collected from Austre Lovénbreen glacier in Svalbard. The two libraries yielded a total of 262 clones belonging to 59 phylotypes. Sequences fell into 10 major lineages of the domain Bacteria, including Proteobacteria (alpha, beta, gamma and delta subdivisions), Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, Chloroflexi, Planctomycetes, Cyanobacteria and candidate division TM7. Among them, Bacteroidetes, Actinobacteria, Alphaproteobacteria and Cyanobacteria were most abundant. UniFrac data showed no significant differences in community composition between the two ice cores. A total of nineteen bacterial strains from the genera Pseudoalteromonas and Psychrobacter were isolated from the ice cores. Phylogenetic and phenotypic analyses revealed a close relationship between the ice core isolates and bacteria in marine environments, indicating a wide distribution of some bacterial phylotypes in both terrestrial and marine ecosystems.

Medicinal benefits of marine invertebrates: sources for discovering natural drug candidates.

PubMed

De Zoysa, Mahanama

2012-01-01

Marine invertebrates are one of the major groups of organisms, which could be diversified under the major taxonomic groups of Porifera, Cnidaria, Mollusca, Arthropoda, Echinodermata, and many other minor phyla. To date, range of medicinal benefits and a significant number of marine natural products (MNPs) have been discovered from marine invertebrates. Seafood diet from edible marine invertebrates such as mollusks and crustaceans has been linked with various medicinal benefits to improve human health. Among marine invertebrates, spongers from phylum Porifera is the most dominant group responsible for discovering large number of MNPs, which have been used as template to develop therapeutic drugs. MNPs isolated from invertebrates have shown wide range of therapeutic properties including antimicrobial, antioxidant, antihypertensive, anticoagulant, anticancer, anti-inflammatory, wound healing and immune modulator, and other medicinal effects. Therefore, marine invertebrates are rich sources of chemical diversity and health benefits for developing drug candidates, cosmetics, nutritional supplements, and molecular probes that can be supported to increase the healthy life span of human. Copyright © 2012 Elsevier Inc. All rights reserved.

Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract

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

Van Passel, Mark W.J.; Kant, Ravi; Palva, Airi

2011-01-01

Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastro-intestinal tract.

A systematic study of the disposition and metabolism of mercury species in mice after exposure to low levels of thimerosal (ethylmercury).

PubMed

Carneiro, Maria Fernanda Hornos; Oliveira Souza, Juliana Maria; Grotto, Denise; Batista, Bruno Lemos; de Oliveira Souza, Vanessa Cristina; Barbosa, Fernando

2014-10-01

Thimerosal (TM) is an ethylmercury (etHg)-containing preservative used in some vaccines despite very limited knowledge on the kinetics and direct interaction/effects in mammals׳ tissues after exposure. Thus, this study aimed to evaluate the kinetics of Hg species in mice in a time course analysis after intramuscular injection of TM, by estimating Hg half-lives in blood and tissues. Mice were exposed to one single intramuscular dose of 20 µg of Hg as TM. Blood, brain, heart, kidney and liver were collected at 0.5 hour (h), 1 h, 8 h, 16 h, 144 h, 720 h and 1980 h after TM exposure (n=4). Hg species in animal tissues were identified and quantified by speciation analysis via liquid chromatography hyphenated with inductively coupled mass spectrometry (LC-ICP-MS). It was found that the transport of etHg from muscle to tissues and its conversion to inorganic Hg (inoHg) occur rapidly. Moreover, the conversion extent is modulated in part by the partitioning between EtHg in plasma and in whole blood, since etHg is rapidly converted in red cells but not in a plasma compartment. Furthermore, the dealkylation mechanism in red cells appears to be mediated by the Fenton reaction (hydroxyl radical formation). Interestingly, after 0.5 h of TM exposure, the highest levels of both etHg and inoHg were found in kidneys (accounting for more than 70% of the total Hg in the animal body), whereas the brain contributed least to the Hg body burden (accounts for <1.0% of total body Hg). Thirty days after TM exposure, most Hg had been excreted while the liver presented the majority of the remaining Hg. Estimated half-lives (in days) were 8.8 for blood, 10.7 for brain, 7.8 for heart, 7.7 for liver and 45.2 for kidney. Taken together, our findings demonstrated that TM (etHg) kinetics more closely approximates Hg(2+) than methylmercury (meHg) while the kidney must be considered a potential target for etHg toxicity. Copyright © 2014 Elsevier Inc. All rights reserved.

Diode-pumped continuous wave tunable and graphene Q-switched Tm:LSO lasers.

PubMed

Feng, T L; Zhao, S Z; Yang, K J; Li, G Q; Li, D C; Zhao, J; Qiao, W C; Hou, J; Yang, Y; He, J L; Zheng, L H; Wang, Q G; Xu, X D; Su, L B; Xu, J

2013-10-21

We have investigated the lasing characteristics of Tm:LSO crystal in three operation regimes: continuous wave (CW), wavelength tunable and passive Q-switching based on graphene. In CW regime, a maximum output power of 0.65 W at 2054.9 nm with a slope efficiency of 21% was achieved. With a quartz plate, a broad wavelength tunable range of 145 nm was obtained, corresponding to a FWHM of 100 nm. By using a graphene saturable absorber mirror, the passively Q-switched Tm:LSO laser produced pulses with duration of 7.8 μs at 2030.8 nm under a repetition rate of 7.6 kHz, corresponding to pulse energy of 14.0 μJ.

A 1-h time interval between a meal containing iron and consumption of tea attenuates the inhibitory effects on iron absorption: a controlled trial in a cohort of healthy UK women using a stable iron isotope.

PubMed

Ahmad Fuzi, Salma F; Koller, Dagmar; Bruggraber, Sylvaine; Pereira, Dora Ia; Dainty, Jack R; Mushtaq, Sohail

2017-12-01

Background: Tea has been shown to be a potent inhibitor of nonheme iron absorption, but it remains unclear whether the timing of tea consumption relative to a meal influences iron bioavailability. Objective: The aim of the study was to investigate the effect of a 1-h time interval of tea consumption on nonheme iron absorption in an iron-containing meal in a cohort of iron-replete, nonanemic female subjects with the use of a stable isotope ( 57 Fe). Design: Twelve women (mean ± SD age: 24.8 ± 6.9 y) were administered a standardized porridge meal extrinsically labeled with 4 mg 57 Fe as FeSO 4 on 3 separate occasions, with a 14-d time interval between each test meal (TM). The TM was administered with water (TM-1), with tea administered simultaneously (TM-2), and with tea administered 1 h postmeal (TM-3). Fasted venous blood samples were collected for iron isotopic analysis and measurement of iron status biomarkers. Fractional iron absorption was estimated by the erythrocyte iron incorporation method. Results: Iron absorption was 5.7% ± 8.5% (TM-1), 3.6% ± 4.2% (TM-2), and 5.7% ± 5.4% (TM-3). Mean fractional iron absorption was found to be significantly higher (2.2%) when tea was administered 1 h postmeal (TM-3) than when tea was administered simultaneously with the meal (TM-2) ( P = 0.046). An ∼50% reduction in the inhibitory effect of tea (relative to water) was observed, from 37.2% (TM-2) to 18.1% (TM-3). Conclusions: This study shows that tea consumed simultaneously with an iron-containing porridge meal leads to decreased nonheme iron absorption and that a 1-h time interval between a meal and tea consumption attenuates the inhibitory effect, resulting in increased nonheme iron absorption. These findings are not only important in relation to the management of iron deficiency but should also inform dietary advice, especially that given to those at risk of deficiency. This trial was registered at clinicaltrials.gov as NCT02365103. © 2017 American Society for Nutrition.

Comparison of a novel high-power blue diode laser (λ=442 nm) with Ho:YAG (λ=2100 nm), Tm fiber (λ=1940 nm), and KTP (λ=532 nm) lasers for soft tissue ablation

NASA Astrophysics Data System (ADS)

Vinnichenko, Victoriya; Kovalenko, Anastasiya; Arkhipova, Valeriya; Yaroslavsky, Ilya; Altshuler, Gregory; Gapontsev, Valentin

2018-02-01

Three lasers were directly compared, including the Ho:YAG laser (λ = 2100 nm), Tm fiber laser (λ = 1940 nm) operating in 3 different modes (CW, regular pulse, and super pulse), and blue diode laser (λ = 442 nm) for vaporization and coagulation efficiency for treating blood-rich soft tissues, ex vivo, in a porcine kidney model at quasi-contact cutting in water. In addition, experimental results were compared with published data on performance of KTP laser (λ = 532 nm) at similar experimental settings (Power = 60 W and cutting speed = 2 mm/s). Tm fiber laser in pulsed mode and blue laser produced highest vaporization rates of 3.7 and 3.4 mm3/s, respectively. Tm fiber laser (in both CW and pulsed modes) also produced the largest coagulation zone among the laser sources tested. A carbonization zone was observed for Tm fiber laser in CW and pulsed modes, as well as for the blue diode laser. Tm fiber laser in super-pulse mode and Ho:YAG laser both resulted in irregular coagulation zones without carbonization. Comparison with known data for KTP laser revealed that tissue effects of the blue laser are similar to that of the KTP laser. These results suggest that the combination of the two lasers (Tm fiber and blue diode) in one system may achieve high cutting efficiency and optimal coagulation for hemostasis during surgical treatment. Ex vivo testing of the combined system revealed feasibility of this approach. The combination of the CW Tm fiber laser (120W) and the blue diode laser (60W) emitting through a combination tip were compared with CW 120 W Tm fiber laser alone and 120 W Ho:YAG laser. Vaporization rates measured 34, 28, and 6 mm3/s, and coagulation zones measured 0.6, 1.3, and 1.7 mm, respectively. A carbonization zone was only observed with CW Tm fiber laser. The vaporization rate of combined CW Tm fiber laser / blue diode laser was comparable to published data for KTP laser for equivalent total power. Thus, high-power blue diode laser, Tm fiber laser, and their combination may provide an alternative to conventional Ho:YAG and KTP lasers for applications in urology and other surgical fields.

White- and blue-light-emitting dysprosium(III) and terbium(III)-doped gadolinium titanate phosphors.

PubMed

Antić, Ž; Kuzman, S; Đorđević, V; Dramićanin, M D; Thundat, T

2017-06-01

Here we report the synthesis and structural, morphological, and photoluminescence analysis of white- and blue-light-emitting Dy 3 + - and Tm 3 + -doped Gd 2 Ti 2 O 7 nanophosphors. Single-phase cubic Gd 2 Ti 2 O 7 nanopowders consist of compact, dense aggregates of nanoparticles with an average size of ~25 nm for Dy 3 + -doped and ~50 nm for Tm 3 + -doped samples. The photoluminescence results indicated that ultraviolet (UV) light excitation of the Dy 3 + -doped sample resulted in direct generation of white light, while a dominant yellow emission was obtained under blue-light excitation. Intense blue light was obtained for Tm 3 + -doped Gd 2 Ti 2 O 7 under UV excitation suggesting that this material could be used as a blue phosphor. Copyright © 2016 John Wiley & Sons, Ltd.

Validity of the iPhone M7 motion co-processor as a pedometer for able-bodied ambulation.

PubMed

Major, Matthew J; Alford, Micah

2016-12-01

Physical activity benefits for disease prevention are well-established. Smartphones offer a convenient platform for community-based step count estimation to monitor and encourage physical activity. Accuracy is dependent on hardware-software platforms, creating a recurring challenge for validation, but the Apple iPhone® M7 motion co-processor provides a standardised method that helps address this issue. Validity of the M7 to record step count for level-ground, able-bodied walking at three self-selected speeds, and agreement with the StepWatch TM was assessed. Steps were measured concurrently with the iPhone® (custom application to extract step count), StepWatch TM and manual count. Agreement between iPhone® and manual/StepWatch TM count was estimated through Pearson correlation and Bland-Altman analyses. Data from 20 participants suggested that iPhone® step count correlations with manual and StepWatch TM were strong for customary (1.3 ± 0.1 m/s) and fast (1.8 ± 0.2 m/s) speeds, but weak for the slow (1.0 ± 0.1 m/s) speed. Mean absolute error (manual-iPhone®) was 21%, 8% and 4% for the slow, customary and fast speeds, respectively. The M7 accurately records step count during customary and fast walking speeds, but is prone to considerable inaccuracies at slow speeds which has important implications for certain patient groups. The iPhone® may be a suitable alternative to the StepWatch TM for only faster walking speeds.

High efficiency 2 micrometer laser utilizing wing-pumped Tm{sup 3+} and a laser diode array end-pumping architecture

DOEpatents

Beach, R.J.

1997-11-18

Wing pumping a Tm{sup 3+} doped, end pumped solid state laser generates 2 {micro}m laser radiation at high average powers with high efficiency. Using laser diode arrays to end-pump the laser rod or slab in the wing of the Tm{sup 3+} absorption band near 785 nm results in 2-for-1 quantum efficiency in Tm{sup 3+} because high Tm{sup 3+} concentrations can be used. Wing pumping allows the thermal power generated in the rod or slab to be distributed over a large enough volume to make thermal management practical in the laser gain medium even at high average power operation. The approach is applicable to CW, Q-switched, and rep-pulsed free-laser operation. 7 figs.

Prediction of pavement remaining service life based on repetition of load and permanent deformation

NASA Astrophysics Data System (ADS)

Usman, R. S.; Setyawan, A.; Suprapto, M.

2018-03-01

One of the methods which was applied in the assessment of flexible pavement performance was mechanistic method assuming structures of road pavement to become multi-layer structure for flexible pavement, that the vehicle load working on the pavement layer under repetition with power failure worth 1 (one) unit which was assumed as evenly distributed static load, and therefore the pavement material would provide response in the form of stress, strain, and deflection. This is closely related in order to assess the structure of flexible pavement and to predict the remaining service life on the roads of Pulau Indah sta 0 + 000 to sta. 0 + 845 in Kota Kupang, Nusa Tenggara Timur. The performance appraisal indicator which was used was fatigue cracking happening bottom of the asphalt layer and permanent deformation (rutting) on the surface of subgrade. The strain estimate on the flexible pavement layer structure needs carefulness and high accuracy and therefore a software like KENPAVE which produces horizontal tensile strain of 8,802E-05 and vertical compressive strain of 2,642E-04 was used. By applying equation of The Asphalt Instituteit was obtained repetition of permit load when reaching fatigue cracking (Nf) was 16.071.516 ESAL and permanent deformation (rutting) was 14.703.867 ESAL and also it was predicted the remaining service life of pavement applied the equation of AASTHO 1993 by considering Traffic Multiplier factor (TM 1.8, TM 1.9 and TM 2.0) obtained the remaining life service due to fatigue of 5.51% in the year of 13th (TM 1.8), 7.95% in the year of12th (TM 1.9) and 3.11% (TM 2.0) in the year of 12th, also the remaining service life due to rutting of 4.69% in the year of 12th(TM 1.8), 7.79% in the year of 11th (TM 1.9), and 2.94 in the year of 11th (TM 2.0).

Prevalence of diabetes mellitus in Chinese children with thalassaemia major.

PubMed

Liang, Yuzhen; Bajoria, Rekha; Jiang, Yan; Su, Hongwei; Pan, Hongfei; Xia, Ning; Chatterjee, Ratna; Lai, Yongrong

2017-06-01

Diabetes mellitus is a common endocrinopathy in patients with β-thalassaemia major (β-TM), which is high prevalent in southern China. This study aimed to determine the cause and prevalence of glycaemic disorders in Chinese children with β-TM. In this prospective study, fasting glucose and insulin (FINS) levels were assessed in 267 β-TM and 80 non-TM control children. Homeostatic model assessment (HOMA) and the quantitative insulin sensitivity check index (QUICKI) were evaluated. Iron overload was assessed by serum ferritin (SF), total units of blood transfused and cardiac T2*. β-TM had higher FPG (P < 0.001), FINS (P < 0.001) and HOMA-IR (P < 0.05), but lower QUICKI (P < 0.01) than those of controls. The impaired fasting glucose (IFG) was present in 30% of children, whereas 2% had diabetes. The prevalence of IFG in β-TM group was higher in children aged >10 years (OR 6.5; 95% CI 3.7-11.4; P < 0.001), SF of >2500 μg/l (OR 4.8; 95% CI 2.1-11.1; P < 0.01), serum ALT levels of >50 IU/l (OR 2.1; 95% CI 1.2-3.7; P < 0.05) and cardiac T2* of <20 ms (OR 3.3; 95% CI 1.7-6.6; P < 0. 01). The children on deferiprone (DFP) had a reduced incidence of glycaemic aberrations than those on other chelating agents (OR 0.4; 95% CI 0.23-0.8; P < 0.05). Our data suggest that IFG occurred in 30% of β TM children, perhaps due to insulin resistance secondary to iron overload. Deferiprone-containing chelating agent may have a protective effect. © 2017 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Plasma homocysteine involved in methylation and expression of thrombomodulin in cerebral infarction.

PubMed

Yang, Zhifu; Wang, Lizhen; Zhang, Wei; Wang, Xinxin; Zhou, Shengnian

2016-05-13

Homocysteine (Hcy) regulates endothelial injury and methylation status of key genes in cerebral ischemia. Thrombomodulin (TM) may be protective against cerebral ischemia by downregulating coagulation. However, it remains unclear whether Hcy involved in methylation and expression of TM in cerebral infarction (CI). Here, we find patients with cerebral infarction had a higher TM methylation level than controls (74.2% vs 47.5%, X(2) = 14.724, P = 0.00), which are positively correlated with plasma levels of tHcy (r = 0.701, P = 0.00) and negatively related to mRNA expression of TM (r = -0.711, P = 0.00). Plasma levels of tHcy (t = 7.566, P = 0.00) and sTM (t = 17.268, P = 0.00) are significantly higher in cases than in controls. Our data indicate hyperhomocysteine leads to hypermethylation of the TM gene and further induces TM gene silencing, which may play an important role in the occurrence and development of CI. Plasma higher concentrations of sTM in cases are not caused by TM expression and may be only a result of Hcy induced endothelial injury. Copyright © 2016 Elsevier Inc. All rights reserved.

Physician Reimbursement in Medicare Advantage Compared With Traditional Medicare and Commercial Health Insurance.

PubMed

Trish, Erin; Ginsburg, Paul; Gascue, Laura; Joyce, Geoffrey

2017-09-01

Nearly one-third of Medicare beneficiaries are enrolled in a Medicare Advantage (MA) plan, yet little is known about the prices that MA plans pay for physician services. Medicare Advantage insurers typically also sell commercial plans, and the extent to which MA physician reimbursement reflects traditional Medicare (TM) rates vs negotiated commercial prices is unclear. To compare prices paid for physician and other health care services in MA, traditional Medicare, and commercial plans. Retrospective analysis of claims data evaluating MA prices paid to physicians and for laboratory services and durable medical equipment between 2007 and 2012 in 348 US core-based statistical areas. The study population included all MA and commercial enrollees with a large national health insurer operating in both markets, as well as a 20% sample of TM beneficiaries. Enrollment in an MA plan. Mean reimbursement paid to physicians, laboratories, and durable medical equipment suppliers for MA and commercial enrollees relative to TM rates for 11 Healthcare Common Procedure Coding Systems (HCPCS) codes spanning 7 sites of care. The sample consisted of 144 million claims. Physician reimbursement in MA was more strongly tied to TM rates than commercial prices, although MA plans tended to pay physicians less than TM. For a mid-level office visit with an established patient (Current Procedural Terminology [CPT] code 99213), the mean MA price was 96.9% (95% CI, 96.7%-97.2%) of TM. Across the common physician services we evaluated, mean MA reimbursement ranged from 91.3% of TM for cataract removal in an ambulatory surgery center (CPT 66984; 95% CI, 90.7%-91.9%) to 102.3% of TM for complex evaluation and management of a patient in the emergency department (CPT 99285; 95% CI, 102.1%-102.6%). However, for laboratory services and durable medical equipment, where commercial prices are lower than TM rates, MA plans take advantage of these lower commercial prices, ranging from 67.4% for a walker (HCPCS code E0143; 95% CI, 66.3%-68.5%) to 75.8% for a complete blood cell count (CPT 85025; 95% CI, 75.0%-76.6%). Traditional Medicare's administratively set rates act as a strong anchor for physician reimbursement in the MA market, although MA plans succeed in negotiating lower prices for other health care services for which TM overpays. Reforms that transition the Medicare program toward some premium support models could substantially affect how physicians and other clinicians are paid.

Petrothermobacter organivorans gen. nov., sp. nov., a thermophilic, strictly anaerobic bacterium of the phylum Deferribacteres isolated from a deep subsurface oil reservoir.

PubMed

Tamazawa, Satoshi; Mayumi, Daisuke; Mochimaru, Hanako; Sakata, Susumu; Maeda, Haruo; Wakayama, Tatsuki; Ikarashi, Masayuki; Kamagata, Yoichi; Tamaki, Hideyuki

2017-10-01

A novel thermophilic, anaerobic, chemoheterotrophic, acetate-oxidizing and iron(III)-, manganese(IV)-, nitrate- and sulfate-reducing bacterium, designated strain ANA T , was isolated from a deep subsurface oil field in Japan (Yabase oil field, Akita Pref.). Cells of strain ANA T were Gram-stain-negative, non-motile, non-spore forming and slightly curved or twisted rods (1.5-5.0 µm long and 0.6-0.7 µm wide). The isolate grew at 25-60 °C (optimum 55 °C) and pH 6.0-8.0 (optimum pH 7.0). The isolate was capable of reducing iron(III), manganese(IV), nitrate and sulfate as an electron acceptor. The isolate utilized a limited range of electron donors such as acetate, lactate, pyruvate and yeast extract for iron reduction. Strain ANA T also used pyruvate, fumarate, succinate, malate, yeast extract and peptone for fermentative growth. The major respiratory quinones were menaquinone-7(H8) and menaquinone-8. The strain contained C18 : 0, iso-C18 : 0 and C16 : 0 as the major cellular fatty acids. The G+C content of the genomic DNA was 34.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ANA T was closely related to Calditerrivibrio nitroreducens in the phylum Deferribacteres with low sequence similarities (89.5 %), and formed a distinct clade within the family Deferribacteraceae. In addition, the isolate is the first sulfate-reducing member of the phylum Deferribacteres. Based on phenotypic, chemotaxonomic and phylogenetic properties, a novel genus and species, Petrothermobacter organivorans gen. nov., sp. nov., is proposed for the isolate (type strain=ANA T = NBRC 112621 T =DSM 105015 T ).

Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria

PubMed Central

Cai, Fei; Axen, Seth D.; Kerfeld, Cheryl A.

2013-01-01

Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria. PMID:23628889

A novel strategy for hemolytic uremic syndrome: successful treatment with thrombomodulin α.

PubMed

Honda, Takashi; Ogata, Shohei; Mineo, Eri; Nagamori, Yukako; Nakamura, Shinya; Bando, Yuki; Ishii, Masahiro

2013-03-01

Hemolytic uremic syndrome (HUS) is a life-threatening infectious disease in childhood for which there is no confirmed therapeutic strategy. Endothelial inflammation leading to microthrombosis formation via complement activation is the main pathology of HUS. Thrombomodulin is an endothelial membrane protein that has anticoagulation and anti-inflammatory effects, including the suppression of complement activity. Recombinant human soluble thrombomodulin (rTM) is a novel therapeutic medicine for disseminated intravascular coagulation. We administered rTM to 3 patients with HUS for 7 days and investigated the outcomes in view of the patients' prognoses, changes in biochemical markers, complications, and adverse effects of rTM. Symptoms and laboratory data improved after initiation of rTM in all 3 patients. Abnormal activation of complements was also dramatically suppressed in 1 patient. The patients recovered without any complications or adverse effects of rTM. They were discharged having normal neurologic status and with no renal dysfunction. To our knowledge, this is the first report of rTM being used to treat HUS. These case reports show the positive effect of rTM in patients with HUS. Randomized controlled studies should be performed to assess the efficacy and safety of rTM for children with HUS.

Evaluation and interpretation of Thematic Mapper ratios in equations for estimating corn growth parameters

NASA Technical Reports Server (NTRS)

Dardner, B. R.; Blad, B. L.; Thompson, D. R.; Henderson, K. E.

1985-01-01

Reflectance and agronomic Thematic Mapper (TM) data were analyzed to determine possible data transformations for evaluating several plant parameters of corn. Three transformation forms were used: the ratio of two TM bands, logarithms of two-band ratios, and normalized differences of two bands. Normalized differences and logarithms of two-band ratios responsed similarly in the equations for estimating the plant growth parameters evaluated in this study. Two-term equations were required to obtain the maximum predictability of percent ground cover, canopy moisture content, and total wet phytomass. Standard error of estimate values were 15-26 percent lower for two-term estimates of these parameters than for one-term estimates. The terms log(TM4/TM2) and (TM4/TM5) produced the maximum predictability for leaf area and dry green leaf weight, respectively. The middle infrared bands TM5 and TM7 are essential for maximizing predictability for all measured plant parameters except leaf area index. The estimating models were evaluated over bare soil to discriminate between equations which are statistically similar. Qualitative interpretations of the resulting prediction equations are consistent with general agronomic and remote sensing theory.

Molecular switches of the κ opioid receptor triggered by 6'-GNTI and 5'-GNTI.

PubMed

Cheng, Jianxin; Sun, Xianqiang; Li, Weihua; Liu, Guixia; Tu, Yaoquan; Tang, Yun

2016-01-08

The κ opioid receptor (κOR) is a member of G-protein-coupled receptors, and is considered as a promising drug target for treating neurological diseases. κOR selective 6'-GNTI was proved to be a G-protein biased agonist, whereas 5'-GNTI acts as an antagonist. To investigate the molecular mechanism of how these two ligands induce different behaviors of the receptor, we built two systems containing the 5'-GNTI-κOR complex and the 6'-GNTI-κOR complex, respectively, and performed molecular dynamics simulations of the two systems. We observe that transmembrane (TM) helix 6 of the κOR rotates about 4.6(o) on average in the κOR-6'-GNTI complex. Detailed analyses of the simulation results indicate that E297(6.58) and I294(6.55) play crucial roles in the rotation of TM6. In the simulation of the κOR-5'-GNTI system, it is revealed that 5'-GNTI can stabilize TM6 in the inactive state form. In addition, the kink of TM7 is stabilized by a hydrogen bond between S324(7.47) and the residue V69(1.42) on TM1.

Novel Pactamycin Analogs Induce p53 Dependent Cell-Cycle Arrest at S-Phase in Human Head and Neck Squamous Cell Carcinoma (HNSCC) Cells

PubMed Central

Guha, Gunjan; Liang, Xiaobo; Kulesz-Martin, Molly F.; Mahmud, Taifo; Indra, Arup Kumar; Ganguli-Indra, Gitali

2015-01-01

Pactamycin, although putatively touted as a potent antitumor agent, has never been used as an anticancer drug due to its high cytotoxicity. In this study, we characterized the effects of two novel biosynthetically engineered analogs of pactamycin, de-6MSA-7-demethyl-7-deoxypactamycin (TM-025) and 7-demethyl-7-deoxypactamycin (TM-026), in head and neck squamous cell carcinoma (HNSCC) cell lines SCC25 and SCC104. Both TM-025 and TM-026 exert growth inhibitory effects on HNSCC cells by inhibiting cell proliferation. Interestingly, unlike their parent compound pactamycin, the analogs do not inhibit synthesis of nascent protein in a cell-based assay. Furthermore, they do not induce apoptosis or autophagy in a dose- or a time-dependent manner, but induce mild senescence in the tested cell lines. Cell cycle analysis demonstrated that both analogs significantly induce cell cycle arrest of the HNSCC cells at S-phase resulting in reduced accumulation of G2/M-phase cells. The pactamycin analogs induce expression of cell cycle regulatory proteins including master regulator p53, its downstream target p21Cip1/WAF1, p27kip21, p19, cyclin E, total and phospho Cdc2 (Tyr15) and Cdc25C. Besides, the analogs mildly reduce cyclin D1 expression without affecting expression of cyclin B, Cdk2 and Cdk4. Specific inhibition of p53 by pifithrin-α reduces the percentage of cells accumulated in S-phase, suggesting contribution of p53 to S-phase increase. Altogether, our results demonstrate that Pactamycin analogs TM-025 and TM-026 induce senescence and inhibit proliferation of HNSCC cells via accumulation in S-phase through possible contribution of p53. The two PCT analogs can be widely used as research tools for cell cycle inhibition studies in proliferating cancer cells with specific mechanisms of action. PMID:25938491

Metagenomics analysis of gut microbiota and immune modulation in zebrafish (Danio rerio) fed chitosan silver nanocomposites.

PubMed

Udayangani, R M C; Dananjaya, S H S; Nikapitiya, Chamilani; Heo, Gang-Joon; Lee, Jehee; De Zoysa, Mahanama

2017-07-01

In this study, we evaluated the effects of chitosan silver nanocomposites (CAgNCs) supplemented diet on gut microbial community, goblet cell density, gut morphometry and mRNA expression of immune related and mucin encoding genes in zebrafish. Zebrafish gut microbiota analysis results clearly showed the reduction of phylum Proteobacteria. However, they remained as the major bacterial group in gut with CAgNCs supplemented diet, while the abundance of phylum Fusobacteria and phylum Bacteroidetes were increased notably compared to the control diet fed fish. Total goblet cell density was significantly increased at 30 and 60 days in CAgNCs supplemented group (1.6-fold and 2.0-fold, respectively) compared to the control group indicating enhanced immune function in the gut. CAgNCs supplementation has also increased villi height significantly in the zebrafish mid gut at the end of 30 (95.5 ± 3.7 μm) and 60 days (144.40 ± 4.8 μm) compared to control diet fed fish at 30 (86.90 ± 3.7 μm) and 60 days (96.2 ± 4.8 μm). Furthermore, mRNA expression of immune related genes such as TNF-α (6.2-fold), IL-10 (5.0-fold), IL-12 (9.2-fold), IRF-1 (5.2-fold), Defbl1 (3-fold), Lyz (5.1-fold) and mucin encoding genes were significantly upregulated (above 2-fold) compared to that of control group. The current study revealed that CAgNCs supplemented diet engenders promising effects on fish gut immunity by enhancing beneficial microbial populations, goblet cell density, villi length, and transcriptional regulation of immune related and mucin encoding genes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Post-marketing surveillance data of thrombomodulin alfa: sub-analysis in patients with sepsis-induced disseminated intravascular coagulation.

PubMed

Eguchi, Yutaka; Gando, Satoshi; Ishikura, Hiroyasu; Saitoh, Daizoh; Mimuro, Jun; Takahashi, Hoyu; Kitajima, Isao; Tsuji, Hajime; Matsushita, Tadashi; Tsujita, Ryuichi; Nagao, Osamu; Sakata, Yoichi

2014-01-01

Thrombomodulin alfa (TM-α, recombinant thrombomodulin) significantly improved disseminated intravascular coagulation (DIC) when compared with heparin therapy in a phase III study. Post-marketing surveillance of TM-α was performed to evaluate the effects and safety in patients with sepsis-induced DIC. From May 2008 to April 2010, a total of 1,787 patients with sepsis-induced DIC treated with TM-α were registered. DIC was diagnosed based on the Japanese Association for Acute Medicine (JAAM) criteria. The DIC resolution and survival rates on day 28 after the last TM-α administration, and changes in DIC, systemic inflammatory response syndrome (SIRS), and sequential organ failure assessment (SOFA) scores and coagulation and inflammation markers were evaluated. The most frequent underlying disease was infectious focus-unknown sepsis (29.8%). The mean ± SD values of age, dose, and the duration of TM-α administration were 64.7 ± 20.3 years, 297.3 ± 111.4 U/kg/day, and 5.6 ± 3.4 days, respectively. A total of 1,320 subjects (73.9%) received combined administration with other anticoagulants. Both coagulation and inflammation markers, such as fibrin/fibrinogen degradation products, prothrombin time ratio, thrombin-antithrombin complex, and C-reactive protein, as well as JAAM DIC, SIRS, and SOFA scores, significantly and simultaneously decreased after TM-α administration (p < 0.001). DIC resolution and 28-day survival rates were 44.4% and 66.0%, respectively. The 28-day survival rate decreased significantly according to the duration of DIC before TM-α administration (p < 0.001). Total adverse drug reactions (ADRs), bleeding ADRs, and serious bleeding adverse events occurred in 126 (7.1%), 98 (5.5%), and 121 (6.8%) subjects, respectively. On day 28, after the last TM-α administration available for an antibody test, only one patient was positive for anti-TM-α antibodies (0.11%). Our results suggest that TM-α is most effective for treating patients with sepsis-induced DIC when administered within the first 3 days after diagnosis.

Live cell imaging of actin dynamics in dexamethasone-treated porcine trabecular meshwork cells.

PubMed

Fujimoto, Tomokazu; Inoue, Toshihiro; Inoue-Mochita, Miyuki; Tanihara, Hidenobu

2016-04-01

The regulation of the actin cytoskeleton in trabecular meshwork (TM) cells is important for controlling outflow of the aqueous humor. In some reports, dexamethasone (DEX) increased the aqueous humor outflow resistance and induced unusual actin structures, such as cross-linked actin networks (CLAN), in TM cells. However, the functions and dynamics of CLAN in TM cells are not completely known, partly because actin stress fibers have been observed only in fixed cells. We conducted live-cell imaging of the actin dynamics in TM cells with or without DEX treatment. An actin-green fluorescent protein (GFP) fusion construct with a modified insect virus was transfected into porcine TM cells. Time-lapse imaging of live TM cells treated with 25 μM Y-27632 and 100 nM DEX was performed using an inverted fluorescence microscope. Fluorescent images were recorded every 15 s for 30 min after Y-27632 treatment or every 30 min for 72 h after DEX treatment. The GFP-actin was expressed in 22.7 ± 10.9% of the transfected TM cells. In live TM cells, many actin stress fibers were observed before the Y-27632 treatment. Y-27632 changed the cell shape and decreased stress fibers in a time-dependent manner. In fixed cells, CLAN-like structures were seen in 26.5 ± 1.7% of the actin-GFP expressed PTM cells treated with DEX for 72 h. In live imaging, there was 28% CLAN-like structure formation at 72 h after DEX treatment, and the lifetime of CLAN-like structures increased after DEX treatment. The DEX-treated cells with CLAN-like structures showed less migration than DEX-treated cells without CLAN-like structures. Furthermore, the control cells (without DEX treatment) with CLAN-like structures also showed less migration than the control cells without CLAN-like structures. These results suggested that CLAN-like structure formation was correlated with cell migration in TM cells. Live cell imaging of the actin cytoskeleton provides valuable information on the actin dynamics in TM cells. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermo-selective Tm(x)Ti(1-x)O(2-x/2) nanoparticles: from Tm-doped anatase TiO2 to a rutile/pyrochlore Tm2Ti2O7 mixture. An experimental and theoretical study with a photocatalytic application.

PubMed

Navas, Javier; Sánchez-Coronilla, Antonio; Aguilar, Teresa; De los Santos, Desireé M; Hernández, Norge C; Alcántara, Rodrigo; Fernández-Lorenzo, Concha; Martín-Calleja, Joaquín

2014-11-07

This is an experimental and theoretical study of thulium doped TiO2 nanoparticles. From an experimental perspective, a method was used to synthesize thulium-doped TiO2 nanoparticles in which Tm(3+) replaces Ti(4+) in the lattice, which to our knowledge has neither been reported nor studied theoretically so far. Different proportions of anatase and rutile phases were obtained at different annealing temperatures, and XRD and Raman spectroscopy also revealed the presence of a pyrochlore phase (Tm2Ti2O7) at 1173 K. Thus, the structure of the Tm-doped nanoparticles was thermally-controlled. Furthermore, XPS showed the presence of Tm(3+) in the samples synthesized, which produces oxygen vacancies to maintain the local neutrality in the lattice. The presence of Tm(3+) in the samples led to changes in the UV-Vis absorption spectra, so they showed photoluminescence properties and new states in the band gap, which produce a new lower energy electronic transition than the main TiO2 one. Periodic DFT calculations were performed to understand the experimentally produced structures. The production of oxygen vacancies was analysed and the changes generated in the structure were fully detailed. The DOS and PDOS analyses confirmed the experimental results obtained using UV-Vis spectroscopy, and showed that the new electronic states in the band gap are due to interactions of the f state of Tm and the p state of O. Likewise, the charge study and the ELF analysis indicate that when Tm is introduced into the TiO2 structure, the Ti-O bond around the oxygen vacancy is strengthened. Finally, an example of a photocatalytic application was developed to show the high efficiency of the samples due to the heterojunction in the interfaces of the phases in the samples, which improved the charge separation and the good charge carrier mobility due to the presence of the pyrochlore phase, as was also shown theoretically.

Threshold voltage control in TmSiO/HfO2 high-k/metal gate MOSFETs

NASA Astrophysics Data System (ADS)

Dentoni Litta, E.; Hellström, P.-E.; Östling, M.

2015-06-01

High-k interfacial layers have been proposed as a way to extend the scalability of Hf-based high-k/metal gate CMOS technology, which is currently limited by strong degradations in threshold voltage control, channel mobility and device reliability when the chemical oxide (SiOx) interfacial layer is scaled below 0.4 nm. We have previously demonstrated that thulium silicate (TmSiO) is a promising candidate as a high-k interfacial layer, providing competitive advantages in terms of EOT scalability and channel mobility. In this work, the effect of the TmSiO interfacial layer on threshold voltage control is evaluated, showing that the TmSiO/HfO2 dielectric stack is compatible with threshold voltage control techniques commonly used with SiOx/HfO2 stacks. Specifically, we show that the flatband voltage can be set in the range -1 V to +0.5 V by the choice of gate metal and that the effective workfunction of the stack is properly controlled by the metal workfunction in a gate-last process flow. Compatibility with a gate-first approach is also demonstrated, showing that integration of La2O3 and Al2O3 capping layers can induce a flatband voltage shift of at least 150 mV. Finally, the effect of the annealing conditions on flatband voltage is investigated, finding that the duration of the final forming gas anneal can be used as a further process knob to tune the threshold voltage. The evaluation performed on MOS capacitors is confirmed by the fabrication of TmSiO/HfO2/TiN MOSFETs achieving near-symmetric threshold voltages at sub-nm EOT.

Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei.

PubMed

Lau, Susanna K P; Lo, George C S; Chow, Franklin W N; Fan, Rachel Y Y; Cai, James J; Yuen, Kwok-Yung; Woo, Patrick C Y

2018-06-12

Talaromyces marneffei is the most important thermal dimorphic fungus causing systemic mycosis in Southeast Asia. We report the discovery of a novel partitivirus, Talaromyces marneffei partitivirus -1 (TmPV1). TmPV1 was detected in 7 (12.7%) of 55 clinical T. marneffei isolates. Complete genome sequencing of the seven TmPV1 isolates revealed two double-stranded RNA (dsRNA) segments encoding RNA-dependent RNA polymerase (RdRp) and capsid protein, respectively. Phylogenetic analysis showed that TmPV1 occupied a distinct clade among the members of the genus Gammapartitivirus Transmission electron microscopy confirmed the presence of isometric, nonenveloped viral particles of 30 to 45 nm in diameter, compatible with partitiviruses, in TmPV1-infected T. marneffei Quantitative reverse transcription-PCR (qRT-PCR) demonstrated higher viral load of TmPV1 in the yeast phase than in the mycelial phase of T. marneffei Two virus-free isolates, PM1 and PM41, were successfully infected by purified TmPV1 using protoplast transfection. Mice challenged with TmPV1-infected T. marneffei isolates showed significantly shortened survival time ( P < 0.0001) and higher fungal burden in organs than mice challenged with isogenic TmPV1-free isolates. Transcriptomic analysis showed that TmPV1 causes aberrant expression of various genes in T. marneffei , with upregulation of potential virulence factors and suppression of RNA interference (RNAi)-related genes. This is the first report of a mycovirus in a thermally dimorphic fungus. Further studies are required to ascertain the mechanism whereby TmPV1 enhances the virulence of T. marneffei in mice and the potential role of RNAi-related genes in antiviral defense in T. marneffei IMPORTANCE Talaromyces marneffei (formerly Penicillium marneffei ) is the most important thermal dimorphic fungus in Southeast Asia, causing highly fatal systemic penicilliosis in HIV-infected and immunocompromised patients. We discovered a novel mycovirus, TmPV1, in seven clinical isolates of T. marneffei TmPV1 belongs to the genus Gammapartitivirus of the family Partitiviridae We showed that TmPV1 enhanced the virulence of T. marneffei in mice, with shortened survival time and higher fungal burden in the organs of mice challenged with TmPV1-infected T. marneffei isolates than in those of mice challenged with virus-free isogenic isolates. Transcriptomics analysis showed that TmPV1 altered the expression of genes involved in various cellular processes in T. marneffei , with upregulation of potential virulence factors and suppression of RNAi machinery which may be involved in antiviral defense. This is the first report of a mycovirus in a thermal dimorphic fungus. The present results offer insights into mycovirus-fungus interactions and pathogenesis of thermal dimorphic fungi. Copyright © 2018 Lau et al.

Neutron Scattering Cross Section Measurements for 169Tm via the (n,n') Technique

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

Alimeti, Afrim; Kegel, Gunter H.R.; Egan, James J.

2005-05-24

The neutron physics group at the University of Massachusetts Lowell (UML) has been involved in a program of scattering cross-section measurements for highly deformed nuclei such as 159Tb, 169Tm, 232Th, 235U, 238U, and 239Pu. Ko et al. have reported neutron inelastic scattering data from 169Tm for states above 100 keV via the (n,n'{gamma}) reaction at incident energies in the 0.2 MeV to 1.0 MeV range. In the present research, in which the time-of-flight method was employed, direct (n,n') measurements of neutrons scattered from 169Tm in the 0.2 to 1.0 MeV range were taken. It requires that our 5.5-MeV Van demore » Graaff accelerator be operated in the pulsed and bunched beam mode producing subnanosecond pulses at a 5-MHz repetition frequency. Neutrons are produced by the 7Li(p,n)7Be reaction using a thin metallic elemental lithium target.« less

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4

PubMed Central

Kranz, Franziska

2016-01-01

G protein coupled receptors (GPCRs) allow for the transmission of signals across biological membranes. For a number of GPCRs, this signaling was shown to be coupled to prior dimerization of the receptor. The chemokine receptor type 4 (CXCR4) was reported before to form dimers and their functionality was shown to depend on membrane cholesterol. Here, we address the dimerization pattern of CXCR4 in pure phospholipid bilayers and in cholesterol-rich membranes. Using ensembles of molecular dynamics simulations, we show that CXCR4 dimerizes promiscuously in phospholipid membranes. Addition of cholesterol dramatically affects the dimerization pattern: cholesterol binding largely abolishes the preferred dimer motif observed for pure phospholipid bilayers formed mainly by transmembrane helices 1 and 7 (TM1/TM5-7) at the dimer interface. In turn, the symmetric TM3,4/TM3,4 interface is enabled first by intercalating cholesterol molecules. These data provide a molecular basis for the modulation of GPCR activity by its lipid environment. PMID:27812115

Structure of the human smoothened receptor 7TM bound to an antitumor agent

PubMed Central

Wang, Chong; Wu, Huixian; Katritch, Vsevolod; Han, Gye Won; Huang, Xi-Ping; Liu, Wei; Siu, Fai Yiu; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.

2013-01-01

The smoothened (SMO) receptor, a key signal transducer in the Hedgehog (Hh) signaling pathway is both responsible for the maintenance of normal embryonic development and implicated in carcinogenesis. The SMO receptor is classified as a class Frizzled (class F) G protein-coupled receptor (GPCR), although the canonical Hh signaling pathway involves the transcription factor Gli and the sequence similarity with class A GPCRs is less than 10%. Here we report the crystal structure at 2.5 Å resolution of the transmembrane domain of the human SMO receptor bound to the small molecule antagonist LY2940680. Although the SMO receptor shares the seven transmembrane helical (7TM) fold, most conserved motifs for class A GPCRs are absent, and the structure reveals an unusually complex arrangement of long extracellular loops stabilized by four disulfide bonds. The ligand binds at the extracellular end of the 7TM bundle and forms extensive contacts with the loops. PMID:23636324

Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

NASA Astrophysics Data System (ADS)

Popova, L. Yu.; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water.

Phonon anomalies in intermediate valent TmXSe and TmSe1 - yTey

NASA Astrophysics Data System (ADS)

Boppart, H.; Treindl, A.; Wachter, P.

1981-03-01

In TmxSe and TmSe1-yTey the degree of valence mixing can be adjusted between nearly 3+ for Tm0.87Se and 2.55+ for TmSe0.7Te0.3. The measurement of sound velocities vL, vTl and vT2 and the evaluation of the Raman effect for various compositions permit the derivation of LA [111] phonon dispersion at critical points in the Brillouin zone. vL decreases with increasing valence mixing. Near the middle of the zone the LA branch gets a dip for intermediate valent compositions, resulting in a characteristic peak in the Ramn spectrum at about 60 cm-1. The elastic constant c12 has been found negative for Tm0.99Se, also at 4.2 K. For uniaxial pressures c12 exhibits strong nonlinearities and even changes sign with pressure in an intermediate valent composition. The optical phonon frequencies, LO (L) also soften proportional with the degree of valence mixing.

Ligand field splittings in core level transitions for transition metal (TM) oxides: Tanabe-Sugano diagrams and (TM) dangling bonds in vacated O-atom defects

NASA Astrophysics Data System (ADS)

Lucovsky, Gerry; Wu, Kun; Pappas, Brian; Whitten, Jerry

2013-04-01

Defect states in the forbidden band-gap below the conduction band edge are active as electron traps in nano-grain high-) transition metal (TM) oxides with thickness >0.3 nm, e.g., ZrO2 and HfO2. These oxides have received considerable attention as gate-dielectrics in complementary metal oxide semiconductor (CMOS) devices, and more recently are emerging as candidates for charge storage and memory devices. To provide a theoretical basis for device functionality, ab-initio many-electron theory is combined with X-ray absorption spectroscopy (XAS) to study O K edge and TM core level transitions. These studies identify ligand field splittings (ΔLF) for defect state features,. When compared with those obtained from O-atom and TM-atom core spectroscopic transitions, this provides direct information about defect state sun-nm bonding arrangements. comparisons are made for (i) elemental TiO2 and Ti2O3 with different formal ionic charges, Ti4+ and Ti3+ and for (ii) Magneli Phase alloys, TinO2n-1, n is an integer 9>=n>3, and (TiO2)x(HfO2)1-x alloys. The alloys display multi-valent behavior from (i) different ionic-charge states, (ii} local bond-strain, and (iii) metallic hopping transport. The intrinsic bonding defects in TM oxides are identified as pairs of singly occupied dangling bonds. For 6-fold coordinated Ti-oxides defect excited states in 2nd derivative O K pre-edge spectra are essentially the same as single Ti-atom d2 transitions in Tanabe-Sugano (T-S) diagrams. O-vacated site defects in 8-fold coordinated ZrO2 and HfO2 are described by d8 T-S diagrams. T-S defect state ordering and splittings are functions of the coordination and symmetry of vacated site bordering TM atoms. ΔLF values from the analysis of T-S diagrams indicate medium range order (MRO) extending to 3rd and 4th nearest-neighbor (NN) TM-atoms. Values are different for 6-fold Ti, and 8-fold ZrO2 and HfO2, and scale inversely with differences in respective formal ionic radii. O-vacated site bonding defects in TM nano-grain oxides are qualitatively similar to vacant-site defects in non-crystalline SiO2 and GeO2 for ulta-thin films, < 0.2 nm thick, and yield similar performance in MOSCAPs on Ge substrates heralding applications in aggressively-scale CMOS devices.

MISSE 6, 7 and 8 Materials Sample Experiments from the International Space Station Materials and Processes Team

NASA Technical Reports Server (NTRS)

Kravchenko, Michael; ORourke, Mary Jane; Golden, Johnny; Finckenor, Miria; Leatherwood, Michael; Alred, John

2010-01-01

The International Space Station Materials and Processes (ISS M&P) team has multiple material samples on MISSE 6, 7 and 8 to observe Low Earth Orbit (LEO) environmental effects on Space Station materials. Optical properties, thickness/mass loss, surface elemental analysis, visual and microscopic analysis for surface change are some of the techniques employed in this investigation. The ISS M&P team has participated in previous MISSE activities in order to better characterize the LEO effects on Space Station materials. This investigation will further this effort. Results for the following MISSE 6 samples materials will be presented: a comparison of anodize and chemical conversion coatings on various aluminum alloys, electroless nickel; AZ93 white ceramic thermal control coating with and without Teflon; Hyzod(TM) polycarbonate used to temporarily protect ISS windows; Russian quartz window material; reformulated Teflon (TM) coated Beta Cloth (Teflon TM without perfluorooctanoic acid (PFOA)) and a Dutch version of beta cloth. Discussion for current and future MISSE materials experiments will be presented. MISSE 7 samples are: deionized water sealed anodized aluminum Photofoil(TM); indium tin oxide (ITO)- coated Kapton(TM) used as thermo-optical surfaces; mechanically scribed tin-plated beryllium-copper samples for "tin pest" growth ( alpha/Beta transformation); Crew Exploration Vehicle (CEV) parachute soft goods. MISSE 8 sample: exposed "scrim cloth" (fiberglass weave) from the ISS solar array wing material, Davlyn fiberglass sleeve material, Permacel and Intertape protective tapes, and ITO-coated Kapton.

Prevalence and clinical characteristics of tori and jaw exostoses in a teaching hospital in Jordan.

PubMed

Sawair, Faleh A; Shayyab, Mohammad H; Al-Rababah, Mohammad A; Saku, Takashi

2009-12-01

To determine the prevalence and clinical characteristics of oral bony outgrowths (OBOs); torus palatinus (TP), torus mandibularis (TM), and exostoses in Jordanian dental patients. This cross-sectional study was conducted between November 1 and December 31, 2008 at the University of Jordan Hospital, Amman, Jordan. Clinical examinations of 618 patients (354 men and 264 women), 10-82 years of age, were conducted to determine the presence of OBOs. There were 239 subjects (38.7%) who had OBOs. Nearly one-third (34.6%) had TP, TM, or both. The prevalence rates were 25.7% for TM, 15.4% for TP, and 14.4% for exostoses. The OBOs were mostly noted in patients in their fifth decade of life, with attrition, clenching, or bruxism. Women had more TP, but gender differences were not statistically significant in cases of TM and exostoses. Most TP were large in size (71.6%), spindle (41.1%), or flat (40%) in shape, and located at the premolar-molar region (45.3%). The TM were mostly medium to large in size (84.9%), bilateral (81.1%), composed of single node (69.2%), and located at the premolar region (65.4%). Of the studied subjects, 7.1% had mandibular buccal exostosis, 10% had maxillary buccal, and 2.4% had palatal exostoses. Statistically significant associations were noticed between the concurrent existence of OBOs. A relatively high prevalence of OBOs was noted, and this should be taken into consideration when planning periodontal surgery and prosthodontic treatment.

Tranexamic Acid-Encapsulating Thermosensitive Liposomes for Site-Specific Pharmaco-Laser Therapy of Port Wine Stains

PubMed Central

van Raath, M. Ingmar; Weijer, Ruud; Nguyen, Gia Hung; Choi, Bernard; de Kroon, Anton I.; Heger, Michal

2017-01-01

Site-specific pharmaco-laser therapy (SSPLT) is a developmental stage treatment modality designed to non-invasively remove superficial vascular pathologies such as port wine stains (PWS) by combining conventional laser therapy with the prior administration of a prothrombotic and/or antifibrinolytic pharmaceutical-containing drug delivery system. For the antifibrinolytic SSPLT component, six different PEGylated thermosensitive liposomal formulations encapsulating tranexamic acid (TA), a potent antifibrinolytic lysine analogue, were characterized for drug:lipid ratio, encapsulation efficiency, size, endovesicular TA concentration (CTA), phase transition temperature (Tm), and assayed for heat-induced TA release. Assays were developed for the quantification of liposomal TA and heat-induced TA release from two candidate formulations. The outcome parameters were then combined with a 3D histological reconstruction of a port wine stain biopsy to extrapolate in vivo posologies for SSPLT. The prime formulation, DPPC:DSPE-PEG2000 (96:4 molar ratio), had a drug:lipid molar ratio of 0.82, an encapsulation efficiency of 1.29%, a diameter of 155 nm, and a CTA of 214 mM. The peak TA release from this formulation (Tm = 42.3 °C) comprised 96% within 2.5 min, whereas this was 94% in 2 min for DPPC:MPPC:DSPE-PEG2000 (86:10:4) liposomes (Tm = 41.5 °C). Computational analysis revealed that <400 DPPC:DSPE-PEG2000 (96:4 molar ratio) liposomes are needed to treat a PWS of 40 cm2, compared to a three-fold greater quantity of DPPC:MPPC:DSPE-PEG2000 (86:10:4) liposomes, indicating that, in light of the assayed parameters and endovascular laser-tissue interactions, the former formulation is most suitable for antifibrinolytic SSPLT. This was further confirmed with experiments involving ex vivo and in vivo liposome-platelet and liposome-red blood cell association as well as uptake and toxicity assays with cultured endothelial cells (HUVECs), macrophages (RAW 264.7), and hepatocytes (HepG2). PMID:29342342

Short-Term Safety and Efficacy of Femoral Vascular Closure after Percutaneous Coronary Intervention with Combination of the Boomerang(TM) Device and Intravenous Protamine Sulfate.

PubMed

Chen, Ching-Pei; Huang, Huang-Kai; Hsia, Chien-Hsun; Chang, Yung-Ming; Lin, Lee-Shin; Lee, Cheng-Liang

2013-11-01

The Cardiva Boomerang(TM) is a device used to perform femoral vascular closure. It facilitates passive hemostasis at the arteriotomy site, leaving no residual foreign body. We performed a controlled, randomized study of 60 patients undergoing percutaneous coronary intervention. Patients were randomized into two groups (30 per group) to undergo vascular closure with the Boomerang(TM) or the Perclose(TM) suture-based device after the intravenous administration of protamine sulfate. We compared overall success rates, patient-reported pain, length of time to achieve hemostasis and mobilization of the patient, and the frequency of complications in the two groups. Overall success rates using the Boomerang(TM) and Perclose(TM) devices were similarly high, at 93% and 97%, respectively. The Boomerang(TM) was significantly quicker to deploy than the PercloseTM, device deployment time, median (Q1-Q3), [2.00 (1.33-2.75) vs. 3.84 (2.75-4.38) mins, p < 0.001)]. The pain score was significantly lower in the Boomerang(TM) group (1.1 ± 1.7 vs. 6.4 ± 2.9, p < 0.001). The time the device remained in the artery and manual compression time were significantly longer with the Boomerang(TM) (p < 0.001), as well as the time taken to achieve hemostasis and time to ambulation. There were no major complications in either group and no significant differences between the groups in the frequency of minor complications. We conclude that when used in combination with intravenous protamine sulfate, the Boomerang(TM) device is as safe and effective as the Perclose(TM) device for femoral vascular closure, but quicker to deploy and less painful to patients. Boomerang; Percutaneous intervention; Vascular closure device.

[Study of serum thrombomodulin(TM) levels in patients with hyper- or hypo- thyroidism].

PubMed

Soma, M; Maeda, Y; Matsuura, R; Sasaki, I; Kasakura, S; Saeki, Y; Ikekubo, K; Ishihara, T; Kurahachi, H; Sasaki, S; Tagami, T; Nakao, K

1997-01-01

We studies a relationship between the serum levels of thrombomodulin(TM) and the thyroid functions. Serum TM levels were measured in 48 patients with Graves' disease, 17 patients with primary hypothyroidism, 7 patients with subacute thyroiditis, 5 patients with painless thyroiditis and 2 patients with systematic Refetoff syndrome. These patients did not have malignant tumor, kidney failure, or blood vessel injury. Control sera were obtained from 42 healthy subjects. Serum levels of TM in patients with untreated Graves' disease were significantly higher(p < 0.001) compared with those in controls. Serum levels of TM in patients with hypothyroidism were not significantly changed as compared with those of controls. There were a positive correlation between the serum levels of TM and FT3 as well as FT4. Serial determinations of the serum levels of TM and thyroid function(FT3, FT4 and TH) in patients with Graves' disease during treatment showed that both the serum levels of TM and thyroid hormones (FT3 and FT4) lowered progressively during treatment. After normalization of serum FT3 and FT4, the serum TM levels returned to normal. However, the serum levels of TM in patients with destructive thyroiditis and Refetoff syndrome were normal in spite of high serum levels of thyroid hormones. These data suggest that an increase in serum levels of TM is not the direct result of thyroid hormones themselves but is the result of the prolonged hypermetabolic state induced by their peripheral activities. Thyroid hormones may stimulate the synthesis or metabolism of TM on the surface of vascular endothelial cells in the patients with Graves' disease.

Regional analysis of tertiary volcanic Calderas (western U.S.) using Landsat Thematic Mapper imagery

NASA Technical Reports Server (NTRS)

Spatz, David M.; Taranik, James V.

1989-01-01

The Landsat Thematic Mapper (TM) imagery of the Basin and Range province of southern Nevada was analyzed to identify and map volcanic rock assemblages at three Tertiary calderas. It was found that the longer-wavelength visible and the NIR TM Bands 3, 5, and 7 provide more effective lithologic discrimination than the shorter-wavelength bands, due partly to deeper penetration of the longer-wavelength bands, resulting in more lithologically driven radiances. Shorter-wavelength TM Bands 1 and 2 are affected more by surficial weathering products including desert varnish which may or may not provide an indirect link to lithologic identity. Guidelines for lithologic analysis of volcanic terrains using Landsat TM imagery are outlined.

Personnel Attrition from Navy Enlisted Initial Technical Training.

DTIC Science & Technology

1979-03-01

total the costs of academic and nonacademic attrition were $8,800,000 anL 5,400,000 respectively. A relatively small number of courses account for a...0014 186 138 74.2 48 25.8 19 6027 FTA-A A113 0010 863 769 89.1 94 10.9 72 6034 TM-SS-TORP-OP A123 0127 141 118 83.7 23 16.3 8 6036 TM-OP-A/S-TORP...856 74 8 45 6034 TM-SF-T)RP-OP A123 0127 ORLANDO 54 25 L 96 152 123 9 6 3 6036 TM-OP-A/S TORP A123 0127 ORLANDO 40 25 L 16 201 192 19 9 2 6041 MN-A

Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces Coelicolor

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

Gao, B.; Sugiman-Marangos, S; Junop, M

2009-01-01

The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.

Seroepidemiology of TmPV1 infection in captive and wild Florida manatees (Trichechus manatus latirostris)

USGS Publications Warehouse

Dona, Maria Gabriella; Rehtanz, Manuela; Adimey, Nicole M.; Bossart, Gregory D.; Jenson, Alfred B.; Bonde, Robert K.; Ghim, Shin-je

2011-01-01

In 1997, cutaneous papillomatosis caused by Florida manatee (Trichechus manatus latirostris [Tm]) papillomavirus 1 (TmPV1) was detected in seven captive manatees at the Homosassa Springs Wildlife State Park, Florida, USA, and, subsequently, in two wild manatees from the adjacent Homosassa River. Since then, papillomatosis has been reported in captive manatees housed in other locations, but not in wild animals. To determine TmPV1 antibody prevalence in captive and wild manatees sampled at various locations throughout Florida coastal regions, virus-like particles, composed of the L1 capsid protein of TmPV1, were generated with a baculovirus expression system and used to measure anti-TmPV1 antibodies in an enzyme-linked immunosorbent assay. Serologic analysis of 156 manatees revealed a TmPV1 antibody prevalence of 26.3%, with no significant difference between captive (n=39) and wild (n=117) manatees (28.2% and 25.6%, respectively). No antibody-positive wild animal showed PV-induced cutaneous lesions, whereas papillomatosis was observed in 72.7% of antibody-positive captive manatees. Our data indicate that Florida manatees living in the wild are naturally infected by TmPV1 but rarely show TmPV1-induced papillomatosis. Hence, it appears that the wild population would not be harmed in a case of contact with captive animals without visible lesions and productive infections, which could be thus released into the wild.

Cytotoxicity and cytokine expression induced by silorane and methacrylate-based composite resins.

PubMed

Longo, Daniele Lucca; Paula-Silva, Francisco Wanderley Garcia; Faccioli, Lucia Helena; Gatón-Hernández, Patrícia Maria; Queiroz, Alexandra Mussolino de; Silva, Léa Assed Bezerra da

2016-01-01

The aim of this study was to evaluate cytotoxicity and cytokine production induced by light-cured or non-light-cured methacrylate-based and silorane composite resins in RAW 264.7 macrophages. Cells were stimulated with the extracts from light-cured or non-light-cured composite resins. After incubation for 24 h, cytotoxicity was assessed with the lactate dehydrogenase (LDH) and methyl thiazolyl tetrazolium (MTT) assays, and total protein was quantified using the Lowry method. TNF-α detection was examined with an enzyme-linked immunosorbent assay (ELISA) conducted with cell supernatants after cell stimulation for 6, 12, and 24 h. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey's post hoc test (α=0.05). KaloreTM and FiltekTM Silorane were cytotoxic with or without light curing (p<0.05) after 24 h of incubation. KaloreTM stimulated the early production of TNF-α in comparison with control (p<0.05), whereas FiltekTM Silorane did not affect TNF-α levels after 6 and 12 h (p>0.05). However, after 24 h FiltekTM Silorane inhibited the production of TNF-α (p<0.05). KaloreTM and FiltekTM Silorane were cytotoxic regardless of light curing. The extract obtained from KaloreTM after 15 days of incubation stimulated the production of TNF-α, unlike that obtained from FiltekTM Silorane.

Seroepidemiology of TmPV1 infection in captive and wild Florida manatees (Trichechus manatus latirostris).

PubMed

Donà, Maria Gabriella; Rehtanz, Manuela; Adimey, Nicole M; Bossart, Gregory D; Jenson, Alfred B; Bonde, Robert K; Ghim, Shin-je

2011-07-01

In 1997, cutaneous papillomatosis caused by Florida manatee (Trichechus manatus latirostris [Tm]) papillomavirus 1 (TmPV1) was detected in seven captive manatees at the Homosassa Springs Wildlife State Park, Florida, USA, and, subsequently, in two wild manatees from the adjacent Homosassa River. Since then, papillomatosis has been reported in captive manatees housed in other locations, but not in wild animals. To determine TmPV1 antibody prevalence in captive and wild manatees sampled at various locations throughout Florida coastal regions, virus-like particles, composed of the L1 capsid protein of TmPV1, were generated with a baculovirus expression system and used to measure anti-TmPV1 antibodies in an enzyme-linked immunosorbent assay. Serologic analysis of 156 manatees revealed a TmPV1 antibody prevalence of 26.3%, with no significant difference between captive (n=39) and wild (n=117) manatees (28.2% and 25.6%, respectively). No antibody-positive wild animal showed PV-induced cutaneous lesions, whereas papillomatosis was observed in 72.7% of antibody-positive captive manatees. Our data indicate that Florida manatees living in the wild are naturally infected by TmPV1 but rarely show TmPV1-induced papillomatosis. Hence, it appears that the wild population would not be harmed in a case of contact with captive animals without visible lesions and productive infections, which could be thus released into the wild.

Comparison of community structures of Candidatus Methylomirabilis oxyfera-like bacteria of NC10 phylum in different freshwater habitats.

PubMed

Shen, Li-Dong; Wu, Hong-Sheng; Gao, Zhi-Qiu; Liu, Xu; Li, Ji

2016-05-09

Methane oxidation coupled to nitrite reduction is mediated by 'Candidatus Methylomirabilis oxyfera' (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4-2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 10(6) and 3.2 × 10(7) copies g(-1) sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

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

Kozubal, Mark; Romine, Margaret F.; Jennings, Ryan

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicate that the replicate assemblies represent a newmore » phylum-level lineage referred to here as 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I CO dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogues active in YNP today.« less

Superoxide Dismutase Protects Cells from DNA Damage Induced by Trivalent Methylated Arsenicals

EPA Science Inventory

Superoxide dismutase (SOD) catalyzes the conversion of superoxide to hydrogen peroxide. Heterozygous mice of strain B6; 129S7-Sod1(tm1Leb)/J were obtained from Jackson Laboratories and bred to produce offspring that were heterozygous (+/Sod1(tm1Leb)), homozygous wild-type (+/+), ...

Towards Longitudinal Mapping of Extracellular pH in Gliomas

PubMed Central

Huang, Yuegao; Coman, Daniel; Herman, Peter; Rao, Jyotsna U.; Maritim, Samuel; Hyder, Fahmeed

2016-01-01

Biosensor Imaging of Redundant Deviation in Shifts (BIRDS), an ultrafast chemical shift imaging technique, requires infusion of paramagnetic probes like 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylene phosphonate (DOTP8−) complexed with thulium (Tm3+) ion (i.e., TmDOTP5−), where the pH-sensitive resonances of hyperfine-shifted nonexchangeable protons contained within the paramagnetic magnetic resonance probe are detected. While imaging extracellular pH (pHe) with BIRDS meets an important cancer research need by mapping the intratumoral-peritumoral pHe gradient, the surgical intervention used to raise the probe’s plasma concentration limits longitudinal scans on the same subject. Here we describe using probenecid (i.e., an organic anion transporter inhibitor) to temporarily restrict renal clearance of TmDOTP5−, thereby facilitating molecular imaging by BIRDS without surgical intervention. Co-infusion of probenecid with TmDOTP5− increased the probe’s distribution into various organs, including the brain, compared with when infusing TmDOTP5− alone. In vivo BIRDS data using probenecid/TmDOTP5− co-infusion method in rats bearing RG2, 9L, and U87 brain tumors showed intratumoral-peritumoral pHe gradients that were unaffected by the probe dose. This co-infusion method can be used for pHe mapping with BIRDS in preclinical models for tumor characterization and therapeutic monitoring given the possibility of repeated scans with BIRDS (e.g., over days and even weeks) in the same subject. The longitudinal pHe readout by probenecid/TmDOTP5− co-infusion method for BIRDS adds translational value in tumor assessment and treatment. PMID:27472471

Molecular modeling of the human vasopressin V2 receptor/agonist complex

NASA Astrophysics Data System (ADS)

Czaplewski, Cezary; Kaźmierkiewicz, Rajmund; Ciarkowski, Jerzy

1998-05-01

The V2 vasopressin renal receptor (V2R), which controls antidiuresis in mammals, is a member of the large family of heptahelical transmembrane (7TM) G protein-coupled receptors (GPCRs). Using the automated GPCR modeling facility available via Internet (http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html) for construction of the 7TM domain in accord with the bovine rhodopsin (RD) footprint, and the SYBYL software for addition of the intra- and extracellular domains, the human V2R was modeled. The structure was further refined and its conformational variability tested by the use of a version of the Constrained Simulated Annealing (CSA) protocol developed in this laboratory. An inspection of the resulting structure reveals that the V2R (likewise any GPCR modeled this way) is much thicker and accordingly forms a more spacious TM cavity than most of the hitherto modeled GPCR constructs do, typically based on the structure of bacteriorhodopsin (BRD). Moreover, in this model the 7TM helices are arranged differently than they are in any BRD-based model. Thus, the topology and geometry of the TM cavity, potentially capable of receiving ligands, is in this model quite different than it is in the earlier models. In the subsequent step, two ligands, the native [arginine8]vasopressin (AVP) and the selective agonist [d-arginine8]vasopressin (DAVP) were inserted, each in two topologically non-equivalent ways, into the TM cavity and the resulting structures were equilibrated and their conformational variabilities tested using CSA as above. The best docking was selected and justified upon consideration of ligand-receptor interactions and structure-activity data. Finally, the amino acid residues were indicated, mainly in TM helices 3-7, as potentially important in both AVP and DAVP docking. Among those Cys112, Val115-Lys116, Gln119, Met123 in helix 3; Glu174 in helix 4; Val206, Ala210, Val213-Phe214 in helix 5; Trp284, Phe287-Phe288, Gln291 in helix 6; and Phe307, Leu310, Ala314 and Asn317 in helix 7 appeared to be the most important ones. Many of these residues are invariant for either the GPCR superfamily or the neurophyseal (vasopressin V2R, V1aR and V1bR and oxytocin OR) subfamily of receptors. Moreover, some of the equivalent residues in V1aR have already been found critical for the ligand affinity [Mouillac et al., J. Biol. Chem, 270 (1995) 25771].

Mechanical Damage of Tympanic Membrane in Relation to Impulse Pressure Waveform – A Study in Chinchillas

PubMed Central

Gan, Rong Z.; Nakmali, Don; Ji, Xiao D.; Leckness, Kegan; Yokell, Zachary

2016-01-01

Mechanical damage to middle ear components in blast exposure directly causes hearing loss, and the rupture of the tympanic membrane (TM) is the most frequent injury of the ear. However, it is unclear how the severity of injury graded by different patterns of TM rupture is related to the overpressure waveforms induced by blast waves. In the present study, the relationship between the TM rupture threshold and the impulse or overpressure waveform has been investigated in chinchillas. Two groups of animals were exposed to blast overpressure simulated in our lab under two conditions: open field and shielded with a stainless steel cup covering the animal head. Auditory brainstem response (ABR) and wideband tympanometry were measured before and after exposure to check the hearing threshold and middle ear function. Results show that waveforms recorded in the shielded case were different from those in the open field and the TM rupture threshold in the shielded case was lower than that in the open field (3.4±0.7 vs. 9.1±1.7 psi or 181±1.6 vs. 190±1.9 dB SPL). The impulse pressure energy spectra analysis of waveforms demonstrates that the shielded waveforms include greater energy at high frequencies than that of the open field waves. Finally, a 3D finite element (FE) model of the chinchilla ear was used to compute the distributions of stress in the TM and the TM displacement with impulse pressure waves. The FE model-derived change of stress in response to pressure loading in the shielded case was substantially faster than that in the open case. This finding provides the biomechanical mechanisms for blast induced TM damage in relation to overpressure waveforms. The TM rupture threshold difference between the open and shielded cases suggests that an acoustic role of helmets may exist, intensifying ear injury during blast exposure. PMID:26807796

Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria

PubMed Central

Polkade, Ashish V.; Mantri, Shailesh S.; Patwekar, Umera J.; Jangid, Kamlesh

2016-01-01

Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit. PMID:26904007

First molecular data on the phylum Loricifera: an investigation into the phylogeny of ecdysozoa with emphasis on the positions of Loricifera and Priapulida.

PubMed

Park, Joong-Ki; Rho, Hyun Soo; Kristensen, Reinhardt Møbjerg; Kim, Won; Giribet, Gonzalo

2006-11-01

Recent progress in molecular techniques has generated a wealth of information for phylogenetic analysis. Among metazoans all but a single phylum have been incorporated into some sort of molecular analysis. However, the minute and rare species of the phylum Loricifera have remained elusive to molecular systematists. Here we report the first molecular sequence data (nearly complete 18S rRNA) for a member of the phylum Loricifera, Pliciloricus sp. from Korea. The new sequence data were analyzed together with 52 other ecdysozoan sequences, with all other phyla represented by three or more sequences. The data set was analyzed using parsimony as an optimality criterion under direct optimization as well as using a Bayesian approach. The parsimony analysis was also accompanied by a sensitivity analysis. The results of both analyses are largely congruent, finding monophyly of each ecdysozoan phylum, except for Priapulida, in which the coelomate Meiopriapulus is separate from a clade of pseudocoelomate priapulids. The data also suggest a relationship of the pseudocoelomate priapulids to kinorhynchs, and a relationship of nematodes to tardigrades. The Bayesian analysis placed the arthropods as the sister group to a clade that includes tardigrades and nematodes. However, these results were shown to be parameter dependent in the sensitivity analysis. The position of Loricifera was extremely unstable to parameter variation, and support for a relationship of loriciferans to any particular ecdysozoan phylum was not found in the data.

Thematic Mapper Data Quality and Performance Assessment in Renewable Resources/agriculture Remote Sensing

NASA Technical Reports Server (NTRS)

Bizzell, R. M.; Prior, H. L.

1984-01-01

It is believed that the increased spatial resolution will provide solutions to proportion estimation error due to mixed pixels, and the increased spectral resolution will provide for the identification of important agricultural features such as crop stage, and condition. The results of analyses conducted relative to these hypothesis from sample segments extracted from the 4-band Detroit scene and the 7-band Mississippi County, Arkansas engineering test scene are described. Several studies were conducted to evaluate the geometric and radiometric performance of the TM to determine data viability for the more pertinent investigations of TM utility. In most cases this requirement was more than sufficiently satisfied. This allowed the opportunity to take advantage of detailed ground observations for several of the sample segments to assess class separability and detection of other important features with TM. The results presented regarding these TM characteristics show that not only is the increased definition of the within scene variance captured by the increased spatial and spectral resolution, but that the mid-IR bands (5 and 7) are necessary for optimum crop type classification. Both qualitative and quantitative results are presented that describe the improvements gained with the TM both relative to the MSS and on its own merit.

PNPLA3 p.I148M variant is associated with greater reduction of liver fat content after bariatric surgery.

PubMed

Krawczyk, Marcin; Jiménez-Agüero, Raúl; Alustiza, José M; Emparanza, José I; Perugorria, María J; Bujanda, Luis; Lammert, Frank; Banales, Jesús M

2016-12-01

Obesity is the major trigger of nonalcoholic fatty liver disease (NAFLD). NAFLD is further favored by the patatin-like phospholipase domain-containing 3 (PNPLA3) p.I148M, transmembrane 6 superfamily member 2 (TM6SF2) p.E167K, and membrane-bound O-acyltransferase domain containing 7 (MBOAT7) rs641738 variants. To investigate the relationship between the PNPLA3, TM6SF2, and MBOAT7 genotypes and the outcomes of bariatric surgery. University hospital. Prospectively we monitored 84 obese individuals (body mass index 35-64 kg/m 2 ) scheduled for bariatric surgery. The PNPLA3 p.I148M, TM6SF2 p.E167K, and MBOAT7 rs641738 variants were genotyped using restriction fragment length polymorphism analysis and TaqMan assays. Hepatic steatosis was determined before surgery using analysis of liver biopsy samples and a novel magnetic resonance imaging-based equation. One year later, steatosis was reevaluated by magnetic resonance imaging. The presence of the PNPLA3 allle [M] was associated with increased hepatic triglyceride content (P = .03), steatosis detected by magnetic resonance imaging (P = 0.04), and decreased serum glucose concentrations (P = .04). Neither variant TM6SF2 nor MBOAT7 increased hepatic steatosis (all P>.05); however, the MBOAT7 polymorphism was associated with increased triglyceride, total cholesterol, low density lipoprotein, and serum glucose levels (all P<.05). Patients carrying the prosteatotic PNPLA3 allele [M] lost more weight (P<.01) and liver fat (P = .04) one year after surgery, as compared to individuals having the common genotype. The PNPLA3 genotype and initial grade of steatosis, but not the TM6SF2 or MBOAT7 variants, were independent predictors of NAFLD improvement (P = .03 and P<.01, respectively). In obese patients, the presence of the PNPLA3 p.I148M allele might be associated with greater improvement of hepatic steatosis after bariatric surgery in comparison to carriers of PNPLA3 wild-type alleles. Copyright © 2016 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

PubMed

Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S

2011-11-01

Members of candidate division OP11 are widely distributed in terrestrial and marine ecosystems, yet little information regarding their metabolic capabilities and ecological role within such habitats is currently available. Here, we report on the microfluidic isolation, multiple-displacement-amplification, pyrosequencing, and genomic analysis of a single cell (ZG1) belonging to candidate division OP11. Genome analysis of the ∼270-kb partial genome assembly obtained showed that it had no particular similarity to a specific phylum. Four hundred twenty-three open reading frames were identified, 46% of which had no function prediction. In-depth analysis revealed a heterotrophic lifestyle, with genes encoding endoglucanase, amylopullulanase, and laccase enzymes, suggesting a capacity for utilization of cellulose, starch, and, potentially, lignin, respectively. Genes encoding several glycolysis enzymes as well as formate utilization were identified, but no evidence for an electron transport chain was found. The presence of genes encoding various components of lipopolysaccharide biosynthesis indicates a Gram-negative bacterial cell wall. The partial genome also provides evidence for antibiotic resistance (β-lactamase, aminoglycoside phosphotransferase), as well as antibiotic production (bacteriocin) and extracellular bactericidal peptidases. Multiple mechanisms for stress response were identified, as were elements of type I and type IV secretion systems. Finally, housekeeping genes identified within the partial genome were used to demonstrate the OP11 affiliation of multiple hitherto unclassified genomic fragments from multiple database-deposited metagenomic data sets. These results provide the first glimpse into the lifestyle of a member of a ubiquitous, yet poorly understood bacterial candidate division.

High quality TmIG films with perpendicular magnetic anisotropy grown by sputtering

NASA Astrophysics Data System (ADS)

Wu, C. N.; Tseng, C. C.; Yeh, S. L.; Lin, K. Y.; Cheng, C. K.; Fanchiang, Y. T.; Hong, M.; Kwo, J.

Ferrimagnetic thulium iron garnet (TmIG) films grown on gadolinium gallium garnet substrates recently showed stress-induced perpendicular magnetic anisotropy (PMA), attractive for realization of quantum anomalous Hall effect (QAHE) of topological insulator (TI) films via the proximity effect. Moreover, current induced magnetization switching of Pt/TmIG has been demonstrated for the development of room temperature (RT) spintronic devices. In this work, high quality TmIG films (about 25nm) were grown by sputtering at RT followed by post-annealing. We showed that the film composition is tunable by varying the growth parameters. The XRD results showed excellent crystallinity of stoichiometric TmIG films with an out-of-plane lattice constant of 1.2322nm, a narrow film rocking curve of 0.017 degree, and a film roughness of 0.2 nm. The stoichiometric films exhibited PMA and the saturation magnetization at RT was 109 emu/cm3 (RT bulk value 110 emu/cm3) with a coercive field of 2.7 Oe. In contrast, TmIG films of Fe deficiency showed in-plane magnetic anisotropy. The high quality sputtered TmIG films will be applied to heterostructures with TIs or metals with strong spin-orbit coupling for novel spintronics.

A Randomized Controlled Trial of Stress Reduction in African Americans Treated for Hypertension for Over One Year

PubMed Central

Schneider, Robert H.; Alexander, Charles N.; Staggers, Frank; Orme-Johnson, David W.; Rainforth, Maxwell; Salerno, John W.; Sheppard, William; Castillo-Richmond, Amparo; Barnes, Vernon A.; Nidich, Sanford I.

2007-01-01

Background Psychosocial stress has been implicated in the disproportionately higher rates of hypertension among African Americans. This randomized controlled trial compared the effects of two stress reduction techniques and a health education control program on hypertension during a period of 1 year in African-American men and women (N = 150, mean age 49 ± 10 years, mean blood pressure (BP) = 142/95 mm Hg) at an urban community health center. Methods Interventions included 20 min twice a day of Transcendental Meditation (TM) or progressive muscle relaxation (PMR), or participation in conventional health education (HE) classes. All subjects continued usual medical care. Outcomes assessed were systolic BP and diastolic BP at 3, 6, 9, and 12 months after treatment, analyzed by repeated measures ANCOVA. Results The TM group showed decreases in systolic BP/diastolic BP of −3.1/−5.7 mm Hg compared to −0.5/−2.9 mm Hg for PMR or HE, (P = .12 to .17 for systolic BP, P = .01 for diastolic BP). In addition the TM group demonstrated reduced use of antihypertensive medication relative to increases for PMR (P = .001) and HE (P = .09) groups. Group analysis by gender showed that women practicing TM had decreased BP (−7.3/−6.9 mm Hg) significantly more than women practicing PMR (0.7/−2.7 mm Hg) or HE (−.07/−3.0 mm Hg) (P .01 to .03). The change in men praticing TM (0.2/−4.7 mm Hg) was greater than men practicing HE (−0.9/−2.0 mm Hg) for diastolic BP only (P = .09,) and not different from PMR men (−2.0/−3.1). Conclusions A selected stress reduction approach, the Transcendental Meditation program, may be useful as an adjunct in the long-term treatment of hypertension in African Americans. PMID:15691622

The effectiveness of digital microscopy as a teaching tool in medical laboratory science curriculum.

PubMed

Castillo, Demetra

2012-01-01

A fundamental component to the practice of Medical Laboratory Science (MLS) is the microscope. While traditional microscopy (TM) is gold standard, the high cost of maintenance has led to an increased demand for alternative methods, such as digital microscopy (DM). Slides embedded with blood specimens are converted into a digital form that can be run with computer driven software. The aim of this study was to investigate the effectiveness of digital microscopy as a teaching tool in the field of Medical Laboratory Science. Participants reviewed known study slides using both traditional and digital microscopy methods and were assessed using both methods. Participants were randomly divided into two groups. Group 1 performed TM as the primary method and DM as the alternate. Group 2 performed DM as the primary and TM as the alternate. Participants performed differentials with their primary method, were assessed with both methods, and then performed differentials with their alternate method. A detailed assessment rubric was created to determine the accuracy of student responses through comparison of clinical laboratory and instructor results. Student scores were reflected as a percentage correct from these methods. This assessment was done over two different classes. When comparing results between methods for each, independent of the primary method used, results were not statistically different. However, when comparing methods between groups, Group 1 (n = 11) (TM = 73.79% +/- 9.19, DM = 81.43% +/- 8.30; paired t10 = 0.182, p < 0.001) showed a significant difference from Group 2 (n = 14) (TM = 85.64% +/- 5.30, DM = 85.91% +/- 7.62; paired t13 = 3.647, p = 0.860). In the subsequent class, results between both groups (n = 13, n = 16, respectively) did not show any significant difference between groups (Group 1 TM = 86.38% +/- 8.17, Group 1 DM = 88.69% +/- 3.86; paired t12 = 1.253, p = 0.234; Group 2 TM = 86.75% +/- 5.37, Group 2 DM = 86.25% +/- 7.01, paired t15 = 0.280, p = 0.784). The data suggest that DM is comparable to TM. DM could be used as an enhancement model after foundational information was provided using TM.

Community pharmacist's responsibilities with regards to traditional medicine/complementary medicine products: A systematic literature review.

PubMed

Ung, Carolina Oi Lam; Harnett, Joanna; Hu, Hao

The use of Traditional Medicine/Complementary Medicine (TM/CM) products has gained popularity in many countries. There is a growing body of evidence to support that concomitant use of TM/CM products with certain pharmaceutical medicines may adversely affect treatment outcomes. There is a general consensus that pharmacists have a role to play in the safe and appropriate use of these products. However, the extent of their involvement and responsibilities are not yet defined. Clear guidelines that inform their duty of care are essential for pharmacists to establish their role in the management of TM/CM product use. The purpose of this study was to determine pharmacist's responsibilities with regards to TM/CM products that have been discussed in the literature since 2000. A literature search in 3 electronic databases (Web of Science, Science Direct and PubMed) was used to extract publications from 2000 to 2015 that related pharmacist to TM/CM products. Out of the 2859 publications extracted for abstract review, 171 documents were selected for full text assessment. 41 publications which reported findings from exploratory studies or discussed pharmacists' responsibilities towards TM/CM products were selected for inclusion in this study. Seven major responsibilities were frequently discussed in the literature: (1) to acknowledge the use; (2) to be knowledgeable about the TM/CM products; (3) to ensure safe use of TM/CM products; (4) to document the use of TM/CM products; (5) to report ADRs related to TM/CM products; (6) to educate about TM/CM products; and (7) to collaborate with other health care professionals. Various forms and levels of pharmacists' responsibilities with TM/CM products have been mentioned in the literature. Subsequent work towards a common consensus must take into account three influential factors strategically: the scope of TM/CM products, objectives of pharmacists' involvement and the perspectives of key stakeholders. Copyright © 2016 Elsevier Inc. All rights reserved.

Screening of proteins based on macro-algae from West Java coast in Indonesian marine as a potential anti-aging agent

NASA Astrophysics Data System (ADS)

Putri, Arlina Prima; Dewi, Rizna Triana; Handayani, Aniek Sri; Harjanto, Sri; Chalid, Mochamad

2018-02-01

Algae has been known as one of the potential marine bio-resources that have been used in many fields such as bio-energy, food, pharmaceutical and medical applications. Study of macro-algae or seaweed for medicine application, in particular, highlights to empower their ingredients as a promising antioxidant like anti-aging agent due to their diversity in biological activity. The tropical climate of Indonesia with the highest marine biodiversity puts this country an auspicious source of numerous alga species as a novel antioxidant source. A Sample of 29 species of macroalgae has been collected from Coast of Pari Island as a part of Seribu Islands, Indonesia. Screening and extracting of aqueous tropical marine alga protein as a potential source for an antioxidant agent has been done by using 2,2-diphenyl-1-picrylhydrazyl scavenging method, and protein contents have been determined by Lowry method. Sample number 26 of the phylum Rhodophyta have 9.00±0.03 % protein content, which is potential for nutritional food in form of nutraceutical. That sample demonstrated the maximum DPPH scavenging activity 79.27±1.81 %. Moreover, crude extract from another species from phylum Rhodophyta had the very lower IC50 (3.4333±0.29 mg/ml) followed by Chlorophyta species (7.1069±1.78 mg/ml). In general, this study found that algae from phylum Rhodophyta possess a high content of protein, high activity towards free radical. Nevertheless, algae acquire the lowest IC50 value not only dominated by Rhodophyta but also from phylum Chlorophyta. The conclusion of this study leads to empowering high antioxidant activity algae as an anti-aging agent, which can be used in pharmaceutical applications. Therefore, the next study should be concerned on the properties of the algae which has been known to be suitable for pharmaceutical fields.

Telangiectatic Matting is Associated with Hypersensitivity and a Bleeding Tendency.

PubMed

Kadam, Pooja; Lim, Jerrick; Paver, Ian; Connor, David E; Parsi, Kurosh

2018-04-01

The aim was to investigate the pathogenesis of telangiectatic matting (TM) and identify possible risk factors. This study had two parts. The clinical records of consecutive patients were retrospectively analysed to identify risk factors for TM. In the second part, the haemostatic and coagulation profile of the subset of patients with TM were analysed and compared with controls using standard coagulation tests, platelet function and a global assay of coagulation (rotational thromboelastometry, ROTEM). In 352 consecutive patients presenting to a phlebology practice, 25 patients had TM (7.1%). All 25 patients were female with the median age of 45 (27-57) years. A comprehensive medical history was taken. Among 27 possible risk factors assessed, statistically significant associations included recurrent epistaxis, easy bruising, hypersensitivity (eczema, hives, hay fever, and rhinitis), previous treatment with sclerotherapy or endovenous laser for lower limb veins, and a family history of telangiectasias. Variables not associated with TM included oral contraceptive intake, hormone replacement therapy, and age. The haemostatic and coagulation profile of 12 patients (6 male and 6 female) with TM did not differ significantly from those without TM. TM is associated with both hypersensitivity and a bleeding tendency. This study revealed no significant increase in the incidence of haemostatic abnormalities in patients with TM compared with the control group. Given the significant association with hypersensitivity disorders, the underlying mast cell hyper-reactivity may contribute to both hypersensitivity and a bleeding tendency and predispose patients to TM. Copyright © 2017 European Society for Vascular Surgery. Published by Elsevier B.V. All rights reserved.

Interacting helical surfaces of the transmembrane segments of subunits a and c' of the yeast V-ATPase defined by disulfide-mediated cross-linking.

PubMed

Kawasaki-Nishi, Shoko; Nishi, Tsuyoshi; Forgac, Michael

2003-10-24

Proton translocation by the vacuolar (H+)-ATPase (or V-ATPase) has been shown by mutagenesis to be dependent upon charged residues present within transmembrane segments of subunit a as well as the three proteolipid subunits (c, c', and c"). Interaction between R735 in TM7 of subunit a and the glutamic acid residue in the middle of TM4 of subunits c and c' or TM2 of subunit c" has been proposed to be essential for proton release to the luminal compartment. In order to determine whether the helical face of TM7 of subunit a containing R735 is capable of interacting with the helical face of TM4 of subunit c' containing the essential glutamic acid residue (Glu-145), cysteine-mediated cross-linking between these subunits in yeast has been performed. Cys-less forms of subunits a and c' as well as forms containing unique cysteine residues were constructed, introduced together into a strain disrupted in both endogenous subunits, and tested for growth at neutral pH, for assembly competence and for cross-linking in the presence of cupric-phenanthroline by SDS-PAGE and Western blot analysis. Four different cysteine mutants of subunit a were each tested pairwise with ten different unique cysteine mutants of subunit c'. Strong cross-linking was observed for the pairs aS728C/c'I142C, aA731C/c'E145C, aA738C/c'F143C, aA738C/c'L147C, and aL739C/c'L147C. Partial cross-linking was observed for an additional 13 of 40 pairs analyzed. When arrayed on a helical wheel diagram, the results suggest that the helical face of TM7 of subunit a containing Arg-735 interacts with the helical face of TM4 of subunit c' centered on Val-146 and bounded by Glu-145 and Leu-147. The results are consistent with a possible rotational flexibility of one or both of these transmembrane segments as well as some flexibility of movement perpendicular to the membrane.

High-power diode-side-pumped rod Tm:YAG laser at 2.07 μm.

PubMed

Wang, Caili; Niu, Yanxiong; Du, Shifeng; Zhang, Chao; Wang, Zhichao; Li, Fangqin; Xu, Jialin; Bo, Yong; Peng, Qinjun; Cui, Dafu; Zhang, Jingyuan; Xu, Zuyan

2013-11-01

We report a high-power diode-laser (LD) side-pumped rod Tm:YAG laser of around 2 μm. The laser was water-cooled at 8°C and yielded a maximum output power of 267 W at 2.07 μm, which is the highest output power for an all solid-state cw 2.07 μm rod Tm:YAG laser reported as far as we know. The corresponding optical-optical conversion efficiency was 20.7%, and the slope efficiency was about 29.8%, respectively.

Predicting the Response of Molluscs to the Impact of Ocean Acidification

PubMed Central

Parker, Laura M.; Ross, Pauline M.; O’Connor, Wayne A.; Pörtner, Hans O.; Scanes, Elliot; Wright, John M.

2013-01-01

Elevations in atmospheric carbon dioxide (CO2) are anticipated to acidify oceans because of fundamental changes in ocean chemistry created by CO2 absorption from the atmosphere. Over the next century, these elevated concentrations of atmospheric CO2 are expected to result in a reduction of the surface ocean waters from 8.1 to 7.7 units as well as a reduction in carbonate ion (CO32−) concentration. The potential impact that this change in ocean chemistry will have on marine and estuarine organisms and ecosystems is a growing concern for scientists worldwide. While species-specific responses to ocean acidification are widespread across a number of marine taxa, molluscs are one animal phylum with many species which are particularly vulnerable across a number of life-history stages. Molluscs make up the second largest animal phylum on earth with 30,000 species and are a major producer of CaCO3. Molluscs also provide essential ecosystem services including habitat structure and food for benthic organisms (i.e., mussel and oyster beds), purification of water through filtration and are economically valuable. Even sub lethal impacts on molluscs due to climate changed oceans will have serious consequences for global protein sources and marine ecosystems. PMID:24832802

Battery of Candidate Physical Tests for Consideration as Occupational Physical Selection Standards for Canadian Forces Trades,

DTIC Science & Technology

1981-07-01

causes a response of the cardio-pulmonary functions similar to that induced by treadmill and bicycle ergometer exercise (89,90). Therefore, a measure of...Flow, and the Blood Pressure and Heart Rate Response to Isometric Exercise . Saint Louis Uni., AFOSR- TR-75-0086, 1974. 51. T.M. PRINTY. A...relationship between the muscle or muscle group and the corresponding lever system responsible for a given movement. Second, the restrictions of the

Arrestin-related proteins mediate pH signaling in fungi.

PubMed

Herranz, Silvia; Rodríguez, José M; Bussink, Henk-Jan; Sánchez-Ferrero, Juan C; Arst, Herbert N; Peñalva, Miguel A; Vincent, Olivier

2005-08-23

Metazoan arrestins bind to seven-transmembrane (7TM) receptors to regulate function. Aspergillus nidulans PalF, a protein involved in the fungal ambient pH signaling pathway, contains arrestin N-terminal and C-terminal domains and binds strongly to two different regions within the C-terminal cytoplasmic tail of the 7TM, putative pH sensor PalH. Upon exposure to alkaline ambient pH, PalF is phosphorylated and, like mammalian beta-arrestins, ubiquitinated in a signal-dependent and 7TM protein-dependent manner. Substitution in PalF of a highly conserved arrestin N-terminal domain Ser residue prevents PalF-PalH interaction and pH signaling in vivo. Thus, PalF is the first experimentally documented fungal arrestin-related protein, dispelling the notion that arrestins are restricted to animal proteomes. Epistasis analyses demonstrate that PalF posttranslational modification is partially dependent on the 4TM protein PalI but independent of the remaining pH signal transduction pathway proteins PalA, PalB, and PalC, yielding experimental evidence bearing on the order of participation of the six components of the pH signal transduction pathway. Our data strongly implicate PalH as an ambient pH sensor, possibly with the cooperation of PalI.

Procedures for using signals from one sensor as substitutes for signals of another

NASA Technical Reports Server (NTRS)

Suits, G.; Malila, W.; Weller, T.

1988-01-01

Long-term monitoring of surface conditions may require a transfer from using data from one satellite sensor to data from a different sensor having different spectral characteristics. Two general procedures for spectral signal substitution are described in this paper, a principal-components procedure and a complete multivariate regression procedure. They are evaluated through a simulation study of five satellite sensors (MSS, TM, AVHRR, CZCS, and HRV). For illustration, they are compared to another recently described procedure for relating AVHRR and MSS signals. The multivariate regression procedure is shown to be best. TM can accurately emulate the other sensors, but they, on the other hand, have difficulty in accurately emulating its shortwave infrared bands (TM5 and TM7).

Double Versus Single Tendon Transfers to Improve Shoulder Function in Brachial Plexus Birth Palsy.

PubMed

Greenhill, Dustin A; Smith, William R; Ramsey, F V; Kozin, Scott H; Zlotolow, Dan A

2017-03-27

In children with brachial plexus birth palsy (BPBP) undergoing tendon transfers to augment shoulder external rotation, it is unclear whether transfer of the latissimus dorsi with its combined latissimus dorsi and teres major (cLT) versus isolated teres major (iTM) tendon transfer yield different outcomes. Records of patients with BPBP who underwent shoulder tendon transfers to augment external rotation were retrospectively reviewed. Transfer type (cLT or iTM) was considered indiscriminate by virtue of surgeon preference. Modified Mallet Scale (mMS) and Active Movement Scale scores were recorded. Patients with <12 months' follow-up, C7 or lower palsy, humeral osteotomy, shoulder procedure(s) within 8 months, microsurgery within 1 year, or recurrent glenohumeral subluxation confirmed by postoperative imaging were excluded. Matched cohorts were identified within each tendon transfer group to yield similar preoperative shoulder function and glenohumeral alignment status. Outcomes for all tendon transfers as well as differences between cLT and iTM cohorts were analyzed. Among 121 cLT and 34 iTM transfers, 49 cLT and 14 iTM met the inclusion criteria. Subsequent matching of cohorts yielded 28 patients (14 cLT and 14 iTM). Average age at time of transfer was 3.0±1.4 years. Follow-up averaged 4.1±3.1 years. There were no statistically significant preoperative differences between cohorts, thus matching criteria were validated. Regardless of tendon(s) transferred, mMS external rotation improved (2.2 to 3.5, P<0.001), whereas mMS internal rotation decreased (3.8 to 3.2, P<0.001). When comparing matched cohorts, cLT transfer produced a greater mMS external rotation improvement than iTM (2.1 vs. 1.5, respectively; P=0.025). Loss of midline function (defined as mMS external rotation <3) occurred in 5 (35.7%) cLT and 2 (14.3%) iTM patients. Both cLT or iTM transfer are effective at augmenting shoulder external rotation in children with C5-C6 BPBP. Furthermore, cLT transfers may yield a larger improvement in external rotation in certain patients. However, both techniques slightly decrease shoulder internal rotation. Given that more total cLT patients lost midline function among matched cohorts, iTM transfer may still be considered when limited midline function is a concern. Level III.

The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus.

PubMed

Sędzielewska Toro, Kinga; Brachmann, Andreas

2016-02-09

Arbuscular mycorrhizal fungi (AMF) form an ecologically important symbiosis with more than two thirds of studied land plants. Recent studies of plant-pathogen interactions showed that effector proteins play a key role in host colonization by controlling the plant immune system. We hypothesise that also for symbiotic-plant interactions the secreted effectome of the fungus is a major component of communication and the conservation level of effector proteins between AMF species may be indicative whether they play a fundamental role. In this study, we used a bioinformatics pipeline to predict and compare the effector candidate repertoire of the two AMF species, Rhizophagus irregularis and Rhizophagus clarus. Our in silico pipeline revealed a list of 220 R. irregularis candidate effector genes that create a valuable information source to elucidate the mechanism of plant infection and colonization by fungi during AMF symbiotic interaction. While most of the candidate effectors show no homologies to known domains or proteins, the candidates with homologies point to potential roles in signal transduction, cell wall modification or transcription regulation. A remarkable aspect of our work is presence of a large portion of the effector proteins involved in symbiosis, which are not unique to each fungi or plant species, but shared along the Glomeromycota phylum. For 95% of R. irregularis candidates we found homologs in a R. clarus genome draft generated by Illumina high-throughput sequencing. Interestingly, 9% of the predicted effectors are at least as conserved between the two Rhizophagus species as proteins with housekeeping functions (similarity > 90%). Therefore, we state that this group of highly conserved effector proteins between AMF species may play a fundamental role during fungus-plant interaction. We hypothesise that in symbiotic interactions the secreted effectome of the fungus might be an important component of communication. Identification and functional characterization of the primary AMF effectors that regulate symbiotic development will help in understanding the mechanisms of fungus-plant interaction.

Newly developed glycogen synthase kinase-3 (GSK-3) inhibitors protect neuronal cells death in amyloid-beta induced cell model and in a transgenic mouse model of Alzheimer's disease.

PubMed

Noh, Min-Young; Chun, Kwangwoo; Kang, Byung Yong; Kim, Heejaung; Park, Ji-Seon; Lee, Han-Chang; Kim, Young-Ha; Ku, Saekwang; Kim, Seung Hyun

2013-05-31

Glycogen synthase kinase-3 (GSK-3) is emerging as a prominent therapeutic target of Alzheimer's disease (AD). A number of studies have been undertaken to develop GSK-3 inhibitors for clinical use. We report two novel GSK-3 inhibitors (C-7a and C-7b) showing good activity and pharmacokinetic (PK) profiles. IC50 of new GSK-3 inhibitors were in the range of 120-130 nM, and they effectively reduced the Aβ-oligomers induced neuronal toxicity. Also, new GSK-3 inhibitors decreased the phosphorylated tau at pThr231, pSer396, pThr181, and pSer202, and inhibited the GSK-3 activity against Aβ-oligomers induced neuronal cell toxicity. In B6;129-Psen1(tm1Mpm) Tg(APPSwe, tauP301L)1Lfa/Mmjax model of AD, oral administration of C-7a (20 mg/kg, 50 mg/kg) showed increased total arm entries and spontaneous alteration of Y-maze which was regarded as short-term memory. In particular, 50 mg/kg C-7a treated mice significantly decreased the level of phosphorylated tau (Ser396) in brain hippocampus. We suggest that new GSK-3 inhibitor (C-7a) is potential candidates for the treatment of AD. Copyright © 2013 The Author. Published by Elsevier Inc. All rights reserved.

Visualizing elemental deposition patterns on carbonaceous anodes from lithium ion batteries: A laser ablation-inductively coupled plasma-mass spectrometry study on factors influencing the deposition of lithium, nickel, manganese and cobalt after dissolution and migration from the Li1[Ni1/3Mn1/3Co1/3]O2 and LiMn1.5 Ni0.5O4 cathode

NASA Astrophysics Data System (ADS)

Schwieters, Timo; Evertz, Marco; Fengler, Alexander; Börner, Markus; Dagger, Tim; Stenzel, Yannick; Harte, Patrick; Winter, Martin; Nowak, Sascha

2018-03-01

In this study, laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is applied to previously aged carbonaceous anodes from lithium ion batteries (LIBs). These electrodes are treated by cyclic aging in a lithium ion cell set-up against Li1[Ni1/3Mn 1/3Co1/3]O2 = NMC111 to elucidate factors that influence transition metal dissolution (TMD) of the cathode and subsequent deposition on the anode. The investigations are carried out by qualitatively visualizing the 7Li and TM patterns (60Ni, 55Mn and 59Co) of whole coin and pouch-bag electrodes. The lithium, as well as the TM amount, found on the anode, is directly correlated to the applied upper cut-off voltage (4.6, 4.7, 4.8 and 4.9 V) showing more deposition of Li and TMs at elevated voltages. While 7Li shows a more homogeneous pattern, the TM distribution is inhomogeneous but showing a similar pattern for all TMs of the same sample. An unequal pressure distribution, resulting in a nonparallel electrode alignment, on the electrode stack is identified to be responsible for the inhomogeneous TM deposition pattern. This uneven electrode orientation results in different diffusion pathways for the TM migration with regard to the spatial distances.

Profiling of wheat class III peroxidase genes derived from powdery mildew-attacked epidermis reveals distinct sequence-associated expression patterns.

PubMed

Liu, Guosheng; Sheng, Xiaoyan; Greenshields, David L; Ogieglo, Adam; Kaminskyj, Susan; Selvaraj, Gopalan; Wei, Yangdou

2005-07-01

A cDNA library was constructed from leaf epidermis of diploid wheat (Triticum monococcum) infected with the powdery mildew fungus (Blumeria graminis f. sp. tritici) and was screened for genes encoding peroxidases. From 2,500 expressed sequence tags (ESTs), 36 cDNAs representing 10 peroxidase genes (designated TmPRX1 to TmPRX10) were isolated and further characterized. Alignment of the deduced amino acid sequences and phylogenetic clustering with peroxidases from other plant species demonstrated that these peroxidases fall into four distinct groups. Differential expression and tissue-specific localization among the members were observed during the B. graminis f. sp. tritici attack using Northern blots and reverse-transcriptase polymerase chain reaction analyses. Consistent with its abundance in the EST collection, TmPRX1 expression showed the highest induction during pathogen attack and fluctuated in response to the fungal parasitic stages. TmPRX1 to TmPRX6 were expressed predominantly in mesophyll cells, whereas TmPRX7 to TmPRX10, which feature a putative C-terminal propeptide, were detectable mainly in epidermal cells. Using TmPRX8 as a representative, we demonstrated that its C-terminal propeptide was sufficient to target a green fluorescent protein fusion protein to the vacuoles in onion cells. Finally, differential expression profiles of the TmPRXs after abiotic stresses and signal molecule treatments were used to dissect the potential role of these peroxidases in multiple stress and defense pathways.

Insights into the transmembrane helix associations of kit ligand by molecular dynamics simulation and TOXCAT.

PubMed

Chai, Mengya; Liu, Bo; Sun, Fude; Wei, Peng; Chen, Peng; Xu, Lida; Luo, Shi-Zhong

2017-07-01

Kit ligand (KITL) plays important roles in cell proliferation, differentiation, and survival via interaction with its receptor Kit. The previous studies demonstrated that KITL formed a noncovalent homodimer through transmembrane (TM) domain; however, the undergoing mechanism of transmembrane association that determines KITL TM dimerization is still not clear. Herein, molecular dynamics (MD) simulation strategy and TOXCAT assay were combined to characterize the dimerization interface and structure of KITL TM in details. KITL TM formed a more energetically favorable noncovalent dimer through a conserved SxxxGxxxG motif in the MD simulation. Furthermore, the TOXCAT results demonstrated that KITL TM self-associated strongly in the bilayer membrane environment. Mutating any one of the small residues Ser11, Gly15 or Gly19 to Ile disrupted KITL TM dimerization dramatically, which further validated our MD simulation results. In addition, our results showed that Tyr22 could help to stabilize the TM interactions via interacting with the phosphoric group in the bilayer membrane. Pro7 did not induce helix kinks or swivel angles in KITL TM, but it was related with the pitch of the turn around this residue so as to affect the dimer formation. Combining the results of computer modeling and experimental mutagenesis studies on the KITL TM provide new insights for the transmembrane helix association of KITL dimerization. Proteins 2017; 85:1362-1370. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

76 FR 288 - National Organic Program (NOP); Sunset Review (2011)

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-04

... Service 7 CFR Part 205 [Document Number AMS-TM-07-0136; TM-07-14PR] RIN 0581-AC77 National Organic Program... (Secretary) by the National Organic Standards Board (NOSB) on November 5, 2009, and April 29, 2010. The... organic production and handling. Consistent with the recommendations from the NOSB, this proposed rule...

Analysis of International Space Station Vehicle Materials on MISSE 6

NASA Technical Reports Server (NTRS)

Finckenor, Miria; Golden, Johnny; Kravchenko, Michael; O'Rourke, Mary Jane

2010-01-01

The International Space Station Materials and Processes team has multiple material samples on MISSE 6, 7 and 8 to observe Low Earth Orbit (LEO) environmental effects on Space Station materials. Optical properties, thickness/mass loss, surface elemental analysis, visual and microscopic analysis for surface change are some of the techniques employed in this investigation. Results for the following MISSE 6 samples materials will be presented: deionized water sealed anodized aluminum; Hyzod(tm) polycarbonate used to temporarily protect ISS windows; Russian quartz window material; Beta Cloth with Teflon(tm) reformulated without perfluorooctanoic acid (PFOA), and electroless nickel. Discussion for current and future MISSE materials experiments will be presented. MISSE 7 samples are: more deionized water sealed anodized aluminum, including Photofoil(tm); indium tin oxide (ITO) over-coated Kapton(tm) used as thermo-optical surfaces; mechanically scribed tin-plated beryllium-copper samples for "tin pest" growth (alpha/beta transformation); and beta cloth backed with a black coating rather than aluminization. MISSE 8 samples are: exposed "scrim cloth" (fiberglass weave) from the ISS solar array wing material, protective fiberglass tapes and sleeve materials, and optical witness samples to monitor contamination.

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

Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.

Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within themore » DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an archaeon from this phylum that is only 0.8 Mb in length and lacks almost all core biosynthetic pathways, but has genes encoding enzymes predicted to interact with bacterial cell walls, consistent with a symbiotic lifestyle. The second new phylum, for which we propose the name Pacearchaeota, was defined based on 46 newly sampled archaeal genomes. This phylum includes the first non-methanogen with an intermediate Type II/III RuBisCO. We also reconstructed a complete (1.24 Mb) genome for another DPANN archaeon, a member of the Diapherotrites phylum. Metabolic prediction and transcriptomic data indicate that this organism has a fermentation-based lifestyle. In fact, genomic analyses consistently indicate lack of recognizable pathways for sulfur, nitrogen, methane, oxygen, and metal cycling, and suggest that symbiotic and fermentation-based lifestyles are widespread across the DPANN superphylum. Thus, as for a recently identified superphylum of bacteria with small genomes and no cultivated representatives, the biogeochemical impacts of this major radiation of archaea are primarily through anaerobic carbon and hydrogen cycling.« less

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

Herbel, J.L.; Hunt, C.D.

An experiment was designed to test the hypothesis that dietary boron impacts upon the function of various coenzymes involved in energy metabolism. In a 2 {times} 7 factorially-arranged experiment, weanling, vitamin D{sub 3}-deprived rats were fed a ground corn-casein-corn oil based diet supplemented with 0 or 2 mg boron/kg and 50% of the requirement for thiamine (TM), riboflavin (RF), pantothenic acid (PA) or pyridoxine (PX); 0% for folic acid (FA) or nicotinic acid (NA). All vitamins were supplemented in adequate amounts in the control diet. At 8 weeks of age, the TM dietary treatment was the one most affected bymore » supplemental dietary boron (SDB). In rats that were fed 50% TM, SDB increased plasma concentrations of triglyceride (TG) and activity of alanine transaminase (ALT), and the liver to body weight (L/B) ratio. However, in the SDB animals, adequate amounts of TM decreased the means of those variables to near that observed in non-SDB rats fed 50% TM. The findings suggest that an interaction between dietary boron and TM affects lipid metabolism.« less

Buffer Optimization of Thermal Melt Assays of Plasmodium Proteins for Detection of Small-Molecule Ligands

PubMed Central

Crowther, Gregory J.; Napuli, Alberto J.; Thomas, Andrew P.; Chung, Diana J.; Kovzun, Kuzma V.; Leibly, David J.; Castaneda, Lisa J.; Bhandari, Janhavi; Damman, Christopher J.; Hui, Raymond; Hol, Wim G. J.; Buckner, Frederick S.; Verlinde, Christophe L. M. J.; Zhang, Zhongsheng; Fan, Erkang; Van Voorhis, Wesley C.

2010-01-01

In the last decade, thermal melt/thermal shift assays have become a common tool for identifying ligands and other factors that stabilize specific proteins. Increased stability is indicated by an increase in the protein's melting temperature (Tm). In optimizing the assays for subsequent screening of compound libraries, it is important to minimize the variability of Tm measurements so as to maximize the assay's ability to detect potential ligands. Here we present an investigation of Tm variability in recombinant proteins from Plasmodium parasites. Ligands of Plasmodium proteins are particularly interesting as potential starting points for drugs for malaria, and new drugs are urgently needed. A single standard buffer (100 mM HEPES, pH 7.5, 150 mM NaCl) permitted estimation of Tm for 58 of 61 Plasmodium proteins tested. However, with several proteins, Tm could not be measured with a consistency suitable for high-throughput screening unless alternative protein-specific buffers were employed. We conclude that buffer optimization to minimize variability in Tm measurements increases the success of thermal melt screens involving proteins for which a standard buffer is suboptimal. PMID:19470714

Lyme Disease and YouTube TM: A Cross-Sectional Study of Video Contents.

PubMed

Basch, Corey H; Mullican, Lindsay A; Boone, Kwanza D; Yin, Jingjing; Berdnik, Alyssa; Eremeeva, Marina E; Fung, Isaac Chun-Hai

2017-08-01

Lyme disease is the most common tick-borne disease. People seek health information on Lyme disease from YouTube TM videos. In this study, we investigated if the contents of Lyme disease-related YouTube TM videos varied by their sources. Most viewed English YouTube TM videos (n = 100) were identified and manually coded for contents and sources. Within the sample, 40 videos were consumer-generated, 31 were internet-based news, 16 were professional, and 13 were TV news. Compared with consumer-generated videos, TV news videos were more likely to mention celebrities (odds ratio [OR], 10.57; 95% confidence interval [CI], 2.13-52.58), prevention of Lyme disease through wearing protective clothing (OR, 5.63; 95% CI, 1.23-25.76), and spraying insecticides (OR, 7.71; 95% CI, 1.52-39.05). A majority of the most popular Lyme disease-related YouTube TM videos were not created by public health professionals. Responsible reporting and creative video-making facilitate Lyme disease education. Partnership with YouTube TM celebrities to co-develop educational videos may be a future direction.

Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

NASA Technical Reports Server (NTRS)

Popova, L. Yu; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

2005-01-01

Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Highly Tm3+ doped germanate glass and its single mode fiber for 2.0 μm laser

PubMed Central

Wen, Xin; Tang, Guowu; Yang, Qi; Chen, Xiaodong; Qian, Qi; Zhang, Qinyuan; Yang, Zhongmin

2016-01-01

Highly Tm3+ doped optical fibers are urgently desirable for 2.0 μm compact single-frequency fiber laser and high-repetition-rate mode-locked fiber laser. Here, we systematically investigated the optical parameters, energy transfer processes and thermal properties of Tm3+ doped barium gallo-germanate (BGG) glasses. Highly Tm3+ doped BGG glass single mode (SM) fibers were fabricated by the rod-in-tube technique. The Tm3+ doping concentration reaches 7.6 × 1020 ions/cm3, being the reported highest level in Tm3+ doped BGG SM fibers. Using ultra short (1.6 cm) as-drawn highly Tm3+ doped BGG SM fiber, a single-frequency fiber laser at 1.95 μm has been demonstrated with a maximum output power of 35 mW when in-band pumped by a home-made 1568 nm fiber laser. Additionally, a multilongitudinal-mode fiber laser at 1.95 μm has also been achieved in a 10 cm long as-drawn active fiber, yielding a maximum laser output power of 165 mW and a slope efficiency of 17%. The results confirm that the as-drawn highly Tm3+ doped BGG SM fibers are promising in applications that require high gain and high power from a short piece of active optical fiber. PMID:26828920

TmCactin plays an important role in Gram-negative and -positive bacterial infection by regulating expression of 7 AMP genes in Tenebrio molitor

PubMed Central

Jo, Yong Hun; Jung Kim, Yu; Beom Park, Ki; Hwan Seong, Jeong; Gon Kim, Soo; Park, Soyi; Young Noh, Mi; Seok Lee, Yong; Soo Han, Yeon

2017-01-01

Cactin was originally identified as an interactor of the Drosophila IκB factor Cactus and shown to play a role in controlling embryonic polarity and regulating the NF-κB signaling pathway. While subsequent studies have identified the roles for Cactin in the mammalian immune response, the immune function of Cactin in insects has not been described yet. Here, we identified a Cactin gene from the mealworm beetle, Tenebrio molitor (TmCactin) and characterized its functional role in innate immunity. TmCactin was highly expressed in prepupa to last instar stages, and its expression was high in the integument and Malpighian tubules of last instar larvae and adults. TmCactin was induced in larvae after infection with different pathogens and detectable within 3 hours of infection. The highest levels of TmCactin expression were detected at 9 hours post infection. TmCactin RNAi significantly decreased the survival rates of larvae after challenge with Escherichia coli and Staphylococcus aureus, but had no significant effect after challenge with Candida albicans. Furthermore, TmCactin RNAi significantly reduced the expression of seven antimicrobial peptide genes (AMPs) after bacterial challenge. Our results suggest that TmCactin may serve as an important regulator of innate immunity, mediating AMP responses against both Gram-positive and Gram-negative bacteria in T. molitor. PMID:28418029

Full-Length Trimeric Influenza Virus Hemagglutinin II Membrane Fusion Protein and Shorter Constructs Lacking the Fusion Peptide or Transmembrane Domain: Hyperthermostability of the Full-Length Protein and the Soluble Ectodomain and Fusion Peptide Make Significant Contributions to Fusion of Membrane Vesicles†

PubMed Central

Ratnayake, Punsisi U.; Ekanayaka, E. A. Prabodha; Komanduru, Sweta S.; Weliky, David P.

2015-01-01

Influenza virus is a Class I enveloped virus which is initially endocytosed into a host respiratory epithelial cell. Subsequent reduction of the pH to the 5–6 range triggers a structural change of the viral hemagglutinin II (HA2) protein, fusion of the viral and endosomal membranes, and release of the viral nucleocapsid into the cytoplasm. HA2 contains fusion peptide (FP), soluble ectodomain (SE), transmembrane (TM), and intraviral domains with respective lengths of ~25, ~160, ~25, and ~10 residues. The present work provides a straightforward protocol for producing and purifying mg quantities of full-length HA2 from expression in bacteria. Biophysical and structural comparisons are made between full-length HA2 and shorter constructs including SHA2 ≡ SE, FHA2 ≡ FP + SE, and SHA2-TM ≡ SE + TM constructs. The constructs are helical in detergent at pH 7.4 and the dominant trimer species. The proteins are highly thermostable in decylmaltoside detergent with Tm > 90 °C for HA2 with stabilization provided by the SE, FP, and TM domains. The proteins are likely in a trimer-of-hairpins structure, the final protein state during fusion. All constructs induce fusion of negatively-charged vesicles at pH 5.0 with much less fusion at pH 7.4. Attractive protein/vesicle electrostatics play a role in fusion, as the proteins are positively-charged at pH 5.0 and negatively-charged at pH 7.4 and the pH-dependence of fusion is reversed for positively-charged vesicles. Comparison of fusion between constructs supports significant contributions to fusion from the SE and the FP with little effect from the TM. PMID:26297995

Full-length trimeric influenza virus hemagglutinin II membrane fusion protein and shorter constructs lacking the fusion peptide or transmembrane domain: Hyperthermostability of the full-length protein and the soluble ectodomain and fusion peptide make significant contributions to fusion of membrane vesicles.

PubMed

Ratnayake, Punsisi U; Prabodha Ekanayaka, E A; Komanduru, Sweta S; Weliky, David P

2016-01-01

Influenza virus is a class I enveloped virus which is initially endocytosed into a host respiratory epithelial cell. Subsequent reduction of the pH to the 5-6 range triggers a structural change of the viral hemagglutinin II (HA2) protein, fusion of the viral and endosomal membranes, and release of the viral nucleocapsid into the cytoplasm. HA2 contains fusion peptide (FP), soluble ectodomain (SE), transmembrane (TM), and intraviral domains with respective lengths of ∼ 25, ∼ 160, ∼ 25, and ∼ 10 residues. The present work provides a straightforward protocol for producing and purifying mg quantities of full-length HA2 from expression in bacteria. Biophysical and structural comparisons are made between full-length HA2 and shorter constructs including SHA2 ≡ SE, FHA2 ≡ FP+SE, and SHA2-TM ≡ SE+TM constructs. The constructs are helical in detergent at pH 7.4 and the dominant trimer species. The proteins are highly thermostable in decylmaltoside detergent with Tm>90 °C for HA2 with stabilization provided by the SE, FP, and TM domains. The proteins are likely in a trimer-of-hairpins structure, the final protein state during fusion. All constructs induce fusion of negatively-charged vesicles at pH 5.0 with much less fusion at pH 7.4. Attractive protein/vesicle electrostatics play a role in fusion, as the proteins are positively-charged at pH 5.0 and negatively-charged at pH 7.4 and the pH-dependence of fusion is reversed for positively-charged vesicles. Comparison of fusion between constructs supports significant contributions to fusion from the SE and the FP with little effect from the TM. Copyright © 2015 Elsevier Inc. All rights reserved.

Correction: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria.

PubMed

Evans, Nathaniel M; Lindner, Alberto; Raikova, Ekaterina V; Collins, Allen G; Cartwright, Paulyn

2009-07-15

Correction to Evans, N.M., Lindner, A., Raikova, E.V., Collins, A.G. and Cartwright, P. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the phylum Cnidaria. BMC Evol Biol, 2008, 8:139.

Computational Thermodynamic Modeling of Hot Corrosion of Alloys Haynes 242 and Hastelloy TM N for Molten Salt Service in Advanced High Temperature Reactors

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

V. Glazoff, Michael; Charit, Indrajt; Sabharwall, Piyush

An evaluation of thermodynamic aspects of hot corrosion of the superalloys Haynes 242 and HastelloyTM N in the eutectic mixtures of KF and ZrF4 is carried out for development of Advanced High Temperature Reactor (AHTR). This work models the behavior of several superalloys, potential candidates for the AHTR, using computational thermodynamics tool (ThermoCalc), leading to the development of thermodynamic description of the molten salt eutectic mixtures, and on that basis, mechanistic prediction of hot corrosion. The results from these studies indicated that the principal mechanism of hot corrosion was associated with chromium leaching for all of the superalloys described above.more » However, HastelloyTM N displayed the best hot corrosion performance. This was not surprising given it was developed originally to withstand the harsh conditions of molten salt environment. However, the results obtained in this study provided confidence in the employed methods of computational thermodynamics and could be further used for future alloy design efforts. Finally, several potential solutions to mitigate hot corrosion were proposed for further exploration, including coating development and controlled scaling of intermediate compounds in the KF-ZrF4 system.« less

Complementary medicine use in patients with head and neck cancer in Ireland.

PubMed

Amin, Mohamed; Glynn, F; Rowley, S; O'Leary, G; O'Dwyer, T; Timon, C; Kinsella, J

2010-08-01

The objectives of the study were: first, to determine the prevalence of traditional medicine (TM) and complementary and alternative medicine (CAM) use in head and neck cancer patients in Ireland; second, to educate ourselves on the plethora of CAM/TM options available to patients outside the dominion of conventional medicine. The study design consisted of a cross-sectional survey carried out in three head and neck cancer centres. Self-administered questionnaires were distributed to 110 head and neck cancer patients attending the three cancer centres and data were collected for statistical analysis. A total of 106 patients completed the questionnaire; 21.7% of the participants used CAM/TM since their diagnosis with head and neck cancer. CAM/TM usage was higher in female (34.3%) than in male patients (16.2%). CAM/TM use was more common in the 41-50-year age group, in patients with higher educational levels and those holding strong religious beliefs, and also in married than single patients. The most common types of CAM/TM used were spiritual and laying on of hands. The most common reasons reported for using CAM/TM were to counteract the ill effects of treatment and increase the body's ability to fight cancer. Sources of information on CAM/TM were friends (65%), family (48%) and media (21%). This survey reveals a high prevalence of CAM/TM use in head and neck cancer patients, hence emphasising the need for otolaryngologists to educate themselves on the various therapies available to be able to provide informative advice. There is an urgent need for evidence-based investigation of various CAM/TM therapies currently offered to patients.

Landsat 4 Thematic Mapper calibration update

USGS Publications Warehouse

Helder, Dennis L.; Malla, Rimy; Mettler, Cory J.; Markham, Brian L.; Micijevic, Esad

2012-01-01

The Landsat 4 Thematic Mapper (TM) collected imagery of the Earth's surface from 1982 to 1993. Although largely overshadowed by Landsat 5 which was launched in 1984, Landsat 4 TM imagery extends the TM-based record of the Earth back to 1982 and also substantially supplements the image archive collected by Landsat 5. To provide a consistent calibration record for the TM instruments, Landsat 4 TM was cross-calibrated to Landsat 5 using nearly simultaneous overpass imagery of pseudo-invariant calibration sites (PICS) in the time period of 1988-1990. To determine if the radiometric gain of Landsat 4 had changed over its lifetime, time series from two PICS locations (a Saharan site known as Libya 4 and a site in southwest North America, commonly referred to as the Sonoran Desert site) were developed. The results indicated that Landsat 4 had been very stable over its lifetime, with no discernible degradation in sensor performance in all reflective bands except band 1. In contrast, band 1 exhibited a 12% decay in responsivity over the lifetime of the instrument. Results from this paper have been implemented at USGS EROS, which enables users of Landsat TM data sets to obtain consistently calibrated data from Landsat 4 and 5 TM as well as Landsat 7 ETM+ instruments.

Landsat 4 results and their implications for agricultural surveys

NASA Technical Reports Server (NTRS)

Erickson, J. D.; Bizzell, R. M.; Pitts, D. E.; Thompson, D. R.

1983-01-01

Progress on defining the minimum Landsat-4 data characteristics needed for agricultural information in the U.S. and assessing the value-added capability of current technology to extract that level of information is reported. Emphasis is laid on the thematic mapper (TM) data and the ground processing facilities. TM data from all 7 bands for a rural Arkansas scene were examined in terms of radiometric, spatial, and geometric fidelity characteristics. Another scene sensed over Iowa was analyzed using three two-channel data sets. Although the TM data were an improvement over MSS data, no value differential was perceived. However, the development of further analysis techniques is still necessary to determine the actual worth of the improved sensor capabilities available with the TM, which actually has an MSS within itself.

Correction: Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

PubMed Central

2009-01-01

Correction to Evans, N.M., Lindner, A., Raikova, E.V., Collins, A.G. and Cartwright, P. Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the phylum Cnidaria. BMC Evol Biol, 2008, 8:139. PMID:19604374

Genomic reconstruction of novel sediment phyla enlightens roles in sedimentary biogeochemical cycling

NASA Astrophysics Data System (ADS)

Baker, B.; Lazar, C.; Seitz, K.; Teske, A.; Hinrichs, K. U.; Dick, G.

2015-12-01

Estuaries are among the most productive habitats on the planet. Microbes in estuary sediments control the turnover of organic carbon, and the anaerobic cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments. We reconstructed 82 bacterial and 24 archaeal high-quality genomes from different redox regimes (sulfate-rich, sulfate-methane transition zone, and methane-rich zones) of estuary sediments. These bacteria belong to 23 distinct groups, including uncultured candidate phyla (eg. KSB1, TA06, and KD3-62), and three newly described phyla (WOR-1, and -2, and -3). The archaea encompass 8 widespread sediment lineages including MGB-D, RC-III and IV, Z7ME43, Parvarchaeota, Lokiarchoaeta (MBG-B), SAGMEG, Bathyarchaeota (groups MCG-1, -6, -7, and -15) and previously unrecognized deeply branched phylum "Thorarchaeota". The uncultured phyla mediate essential biogeochemical processes of the estuarine environment. Z7ME43 archaea have genes for S disproportionation (S0 reduction and thiosulfate reduction and oxidation). SAGMEG appear to be strict anaerobes capable of coupling CO/H2 oxidation to either S0 or nitrite reduction and have novel RubisCO genes for carbon fixation. Thorarchaeota contain pathways for acetate production from the degradation of detrital proteins and intermediate S cycling. Furthermore, the gene content of this group revealed links in the evolutionary histories of archaea and eukaryotes. This dataset extents our knowledge of the metabolic potential of several uncultured phyla. We were able to chart the flow of carbon and nutrients through the multiple layers of bacterial processing and reveal potential ecological interactions within the communities.

Field comparison of OraQuick® ADVANCE Rapid HIV-1/2 antibody test and two blood-based rapid HIV antibody tests in Zambia

PubMed Central

2012-01-01

Background Zambia’s national HIV testing algorithm specifies use of two rapid blood based antibody assays, Determine®HIV-1/2 (Inverness Medical) and if positive then Uni-GoldTM Recombigen HIV-1/2 (Trinity Biotech). Little is known about the performance of oral fluid based HIV testing in Zambia. The aims of this study are two-fold: 1) to compare the diagnostic accuracy (sensitivity and specificity) under field conditions of the OraQuick® ADVANCE® Rapid HIV-1/2 (OraSure Technologies, Inc.) to two blood-based rapid antibody tests currently in use in the Zambia National Algorithm, and 2) to perform a cost analysis of large-scale field testing employing the OraQuick®. Methods This was a operational retrospective research of HIV testing and questionnaire data collected in 2010 as part of the ZAMSTAR (Zambia South Africa TB and AIDS reduction) study. Randomly sampled individuals in twelve communities were tested consecutively with OraQuick® test using oral fluid versus two blood-based rapid HIV tests, Determine® and Uni-GoldTM. A cost analysis of four algorithms from health systems perspective were performed: 1) Determine® and if positive, then Uni-GoldTM (Determine®/Uni-GoldTM); based on current algorithm, 2) Determine® and if positive, then OraQuick® (Determine®/OraQuick®), 3) OraQuick® and if positive, then Determine® (OraQuick®/Determine®), 4) OraQuick® and if positive, then Uni-GoldTM (OraQuick®/Uni-GoldTM). This information was then used to construct a model using a hypothetical population of 5,000 persons with varying prevalence of HIV infection from 1–30%. Results 4,458 participants received both a Determine® and OraQuick® test. The sensitivity and specificity of the OraQuick® test were 98.7 (95%CI, 97.5–99.4) and 99.8 (95%CI, 99.6–99.9), respectively when compared to HIV positive serostatus. The average unit costs per algorithm were US$3.76, US$4.03, US$7.35, and US$7.67 for Determine®/Uni-GoldTM, Determine®/OraQuick®, OraQuick®/Determine®, and OraQuick®/Uni-GoldTM, respectively, for an HIV prevalence of 15%. Conclusions An alternative HIV testing algorithm could include OraQuick® test which had a high sensitivity and specificity. The current Determine®/Uni-GoldTM testing algorithm is the least expensive when compared to Determine®/OraQuick®, OraQuick®/Determine®, and OraQuick®/Uni-GoldTM in the Zambian setting. From our field experience, oral fluid based testing offers many advantages over blood-based testing, especially with self testing on the horizon. PMID:22871032

DIME Participant Builds a Potential Drop Tower Candidate

NASA Technical Reports Server (NTRS)

2002-01-01

A student assembles a Lego (TM) Challenge device designed to operate in the portable drop tower demonstrator as part of the second Dropping in a Microgravity Environment (DIME) competition held April 23-25, 2002, at NASA's Glenn Research Center. Competitors included two teams from Sycamore High School, Cincinnati, OH, and one each from Bay High School, Bay Village, OH, and COSI Academy, Columbus, OH. DIME is part of NASA's education and outreach activities. Details are on line at http://microgravity.grc.nasa.gov/DIME_2002.html.

ICI 56,780 Optimization: Structure-Activity Relationship Studies of 7-(2-Phenoxyethoxy)-4(1H)-quinolones with Antimalarial Activity.

PubMed

Maignan, Jordany R; Lichorowic, Cynthia L; Giarrusso, James; Blake, Lynn D; Casandra, Debora; Mutka, Tina S; LaCrue, Alexis N; Burrows, Jeremy N; Willis, Paul A; Kyle, Dennis E; Manetsch, Roman

2016-07-28

Though malaria mortality rates are down 48% globally since 2000, reported occurrences of resistance against current therapeutics threaten to reverse that progress. Recently, antimalarials that were once considered unsuitable therapeutic agents have been revisited to improve physicochemical properties and efficacy required for selection as a drug candidate. One such compound is 4(1H)-quinolone ICI 56,780, which is known to be a causal prophylactic that also displays blood schizonticidal activity against P. berghei. Rapid induction of parasite resistance, however, stalled its further development. We have completed a full structure-activity relationship study on 4(1H)-quinolones, focusing on the reduction of cross-resistance with atovaquone for activity against the clinical isolates W2 and TM90-C2B, as well as the improvement of microsomal stability. These studies revealed several frontrunner compounds with superb in vivo antimalarial activity. The best compounds were found to be curative with all mice surviving a Plasmodium berghei infection after 30 days.

Grapevine MLO candidates required for powdery mildew pathogenicity?

PubMed Central

Feechan, Angela; Jermakow, Angelica M

2009-01-01

MLOs belong to the largest family of seven-transmembrane (7TM) domain proteins found in plants. The Arabidopsis and rice genomes contain 15 and 12 MLO family members, respectively. Although the biological function of most MLO family members remains elusive, a select group of MLO proteins have been demonstrated to negatively regulate defence responses to the obligate biotrophic pathogen, powdery mildew, thereby acting as “susceptibility” genes. Recently we identified a family of 17 putative VvMLO genes in the genome of the cultivated winegrape species, Vitis vinifera. Expression analysis indicated that the VvMLO family members respond differently to biotic and abiotic stimuli. Infection of V. vinifera by grape powdery mildew (Erysiphe necator) specifically upregulates four VvMLO genes that are orthologous to the Arabidopsis and tomato MLOs previously demonstrated to be required for powdery mildew susceptibility. We postulate that one or more of these E. necator responsive VvMLOs may have a role in the powdery mildew susceptibility of grapevine. PMID:19816131

Toxic Hazards in Aviation.

DTIC Science & Technology

1981-04-01

TM T7M T7T2M Skin Leiomyoma (B) 0/170 1/161 0/146 0/147 Squamous Cell Carcinoma (P) 0/170 1/161 0/146 0/147 Trichoepithelioma (B) 0/170 1/161 0/146 0...The activity’ Is expressed as~I OT 1’,. 4C ~i- ’outined Iln Figure l, egend. W, ENFO TM ,miue Bi8-1 TOXICITE DES GAZ OE DECOMiPOSITION THERIQgUE DES...ntWest que tdc 7 p. cent lorsqtion passe de 1 ’air ht ut) inlanqe bi 1 p). cent tie [C02?. I ’ aoiqment at ion det I at fr~tilerrice reap irat oi re

Cytotoxicity and cytokine expression induced by silorane and methacrylate-based composite resins

PubMed Central

LONGO, Daniele Lucca; PAULA-SILVA, Francisco Wanderley Garcia; FACCIOLI, Lucia Helena; GATÓN-HERNÁNDEZ, Patrícia Maria; de QUEIROZ, Alexandra Mussolino; da SILVA, Léa Assed Bezerra

2016-01-01

ABSTRACT The successful use of composite resins in Dentistry depends on physicochemical properties, but also on the biological compatibility of resins, because of the close association between pulp and dentin. Objective The aim of this study was to evaluate cytotoxicity and cytokine production induced by light-cured or non-light-cured methacrylate-based and silorane composite resins in RAW 264.7 macrophages. Material and Methods Cells were stimulated with the extracts from light-cured or non-light-cured composite resins. After incubation for 24 h, cytotoxicity was assessed with the lactate dehydrogenase (LDH) and methyl thiazolyl tetrazolium (MTT) assays, and total protein was quantified using the Lowry method. TNF-α detection was examined with an enzyme-linked immunosorbent assay (ELISA) conducted with cell supernatants after cell stimulation for 6, 12, and 24 h. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc test (α=0.05). Results KaloreTM and FiltekTM Silorane were cytotoxic with or without light curing (p<0.05) after 24 h of incubation. KaloreTM stimulated the early production of TNF-α in comparison with control (p<0.05), whereas FiltekTM Silorane did not affect TNF-α levels after 6 and 12 h (p>0.05). However, after 24 h FiltekTM Silorane inhibited the production of TNF-α (p<0.05). Conclusions KaloreTM and FiltekTM Silorane were cytotoxic regardless of light curing. The extract obtained from KaloreTM after 15 days of incubation stimulated the production of TNF-α, unlike that obtained from FiltekTM Silorane. PMID:27556204

Label-free imaging of trabecular meshwork cells using Coherent Anti-Stokes Raman Scattering (CARS) microscopy

PubMed Central

Lei, Tim C.; Ammar, David A.; Masihzadeh, Omid; Gibson, Emily A.

2011-01-01

Purpose To image the human trabecular meshwork (TM) using a non-invasive, non-destructive technique without the application of exogenous label. Methods Flat-mounted TM samples from a human cadaver eye were imaged using two nonlinear optical techniques: coherent anti-Stokes Raman scattering (CARS) and two-photon autofluorescence (TPAF). In TPAF, two optical photons are simultaneously absorbed and excite molecules in the sample that then emit a higher energy photon. The signal is predominately from collagen and elastin. The CARS technique uses two laser frequencies to specifically excite carbon-hydrogen bonds, allowing the visualization of lipid-rich cell membranes. Multiple images were taken along an axis perpendicular to the surface of the TM for subsequent analysis. Results Analysis of multiple TPAF images of the TM reveals the characteristic overlapping bundles of collagen of various sizes. Simultaneous CARS imaging revealed elliptical structures of ~7×10 µm in diameter populating the meshwork which were consistent with TM cells. Irregularly shaped objects of ~4 µm diameter appeared in both the TPAF and CARS channels, and are consistent with melanin granules. Conclusions CARS techniques were successful in imaging live TM cells in freshly isolated human TM samples. Similar images have been obtained with standard histological techniques, however the method described here has the advantage of being performed on unprocessed, unfixed tissue free from the potential distortions of the fine tissue morphology that can occur due to infusion of fixatives and treatment with alcohols. CARS imaging of the TM represents a new avenue for exploring details of aqueous outflow and TM cell physiology. PMID:22025898

A systematic study of the disposition and metabolism of mercury species in mice after exposure to low levels of thimerosal (ethylmercury)

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

Carneiro, Maria Fernanda Hornos, E-mail: mafehoca@fcfrp.usp.br; Oliveira Souza, Juliana Maria, E-mail: souza.jmo@gmail.com; Grotto, Denise, E-mail: denise.grotto@prof.uniso.br

Thimerosal (TM) is an ethylmercury (etHg)-containing preservative used in some vaccines despite very limited knowledge on the kinetics and direct interaction/effects in mammals' tissues after exposure. Thus, this study aimed to evaluate the kinetics of Hg species in mice in a time course analysis after intramuscular injection of TM, by estimating Hg half-lives in blood and tissues. Mice were exposed to one single intramuscular dose of 20 µg of Hg as TM. Blood, brain, heart, kidney and liver were collected at 0.5 hour (h), 1 h, 8 h, 16 h, 144 h, 720 h and 1980 h after TM exposuremore » (n=4). Hg species in animal tissues were identified and quantified by speciation analysis via liquid chromatography hyphenated with inductively coupled mass spectrometry (LC–ICP-MS). It was found that the transport of etHg from muscle to tissues and its conversion to inorganic Hg (inoHg) occur rapidly. Moreover, the conversion extent is modulated in part by the partitioning between EtHg in plasma and in whole blood, since etHg is rapidly converted in red cells but not in a plasma compartment. Furthermore, the dealkylation mechanism in red cells appears to be mediated by the Fenton reaction (hydroxyl radical formation). Interestingly, after 0.5 h of TM exposure, the highest levels of both etHg and inoHg were found in kidneys (accounting for more than 70% of the total Hg in the animal body), whereas the brain contributed least to the Hg body burden (accounts for <1.0% of total body Hg). Thirty days after TM exposure, most Hg had been excreted while the liver presented the majority of the remaining Hg. Estimated half-lives (in days) were 8.8 for blood, 10.7 for brain, 7.8 for heart, 7.7 for liver and 45.2 for kidney. Taken together, our findings demonstrated that TM (etHg) kinetics more closely approximates Hg{sup 2+} than methylmercury (meHg) while the kidney must be considered a potential target for etHg toxicity. - Highlights: • Ethylmercury is rapidly converted to inorganic mercury. • Hg substantially accumulates in kidney with a terminal half-life of 45.2 d. • The dealkylation of ethylmercury occurs in red blood cells but not in plasma. • Hydroxyl radical is probably the main effector of this dealkylation. • Kidney must be considered a potential target for ethylmercury toxicity.« less

Pattern of traditional medicine use by adult Saudi patients with neurological disorders.

PubMed

Mohammad, Yousef; Al-Ahmari, Ahmed; Al-Dashash, Fahad; Al-Hussain, Fawaz; Al-Masnour, Firas; Masoud, Abdullah; Jradi, Hoda

2015-04-01

Traditional medicine (TM) has been established as a two-edged sword. On one edge numerous forms of TM have been proven safe and effective, while on the other edge various modes of TM have been shown to be futile and potentially dangerous. Resorting to TM, especially for chronic diseases, is common world-wide and includes Saudi Arabia. Most neurological diseases are chronic. No data is available on the utilization of TM among patients with neurological disorders. We conducted this study to assess for the prevalence, pattern, perception and triggers for TM use by the adult Saudi patients with neurological disorders. A survey written in Arabic and comprised of 15 questions was used to collect data on the practice of TM among the neurology patients of King Saud University Ambulatory Clinic. The questions in the survey pertain mainly to the frequency of TM practice, its form and the patient's opinion of this practice. The data was collected through a face to face interview by three medical students who were instructed on the survey questions prior to the launch of the study. 292 patients completed the survey (35.9% males and 64.0% females). 67% (n = 196) of the sample used TM. Cupping or what is commonly known as "hojamah" was the most prevalent method (45.4%) followed by herbs, skin cauterization and the Reciting of the Holy Quran (42.3%, 33.7% and 20.4% respectively). The prevalence of TM use did not differ across gender (chi-sq = 2.02; p-value = 0.15), level of education (chi-sq = 4.02; p-value = 0.40), health status (chi-sq = 2.29; p-value = 0.68), age groups (chi-sq = 5.12; p-value = 0.16), or perception toward TM (chi-sq = 2.67; p-value = 0.26) in this population. The practice of TM is common among the neurology patients of Saudi Arabia. Cupping, herbs, and skin cauterization, which can be harmful when wrongly employed, are frequently utilized in this patient population. Measures and policies to endorse the appropriate use of TM by Saudi society must be implemented promptly.

Polarimetric Interferometric Experiment Trials for Years 2001 and 2002: Experiment Design Ground Truthing Data Quality and Analysis

DTIC Science & Technology

2003-09-01

type as staged at sites one and two. -T.N Jt- ’I,-’ 7 "A` fl-b - "’, j’¾ liti -- S Z ANZIC D -j Z" itN L/ ’ Hrt Irk ~ SG~i’ 18 DRDC Otaw TM 2003142...initialisms .............................................................. 129 Vi DRDC Ottawa TM 2003-142 List of figures... - s - f ur e...be found in [6, 7, 8, 9]. PolSAR utilizes the information available from the polarimetric ellipse to determine the physical structure( s ) that the

Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor.

PubMed

Wootten, Denise; Reynolds, Christopher A; Smith, Kevin J; Mobarec, Juan C; Furness, Sebastian G B; Miller, Laurence J; Christopoulos, Arthur; Sexton, Patrick M

2016-10-15

Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation. Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity. Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues located towards the TM helical boundaries of Class B GPCRs that are important for GLP-1 receptor stability and/or controlling signalling specificity and biased agonism. This includes (i) three positively charged residues (R3.30 227 , K4.64 288 , R5.40 310 ) located at the extracellular boundaries of TMs 3, 4 and 5 that are predicted in molecular models to stabilise extracellular loop 2, a crucial domain for ligand affinity and receptor activation; (ii) a predicted hydrogen bond network between residues located in TMs 2 (R2.46 176 ), 6 (R6.37 348 ) and 7 (N7.61 406 and E7.63 408 ) at the cytoplasmic face of the receptor that is important for stabilising the inactive receptor and directing signalling specificity, (iii) residues at the bottom of TM 5 (R5.56 326 ) and TM6 (K6.35 346 and K6.40 351 ) that are crucial for receptor activation and downstream signalling; (iv) residues predicted to be involved in stabilisation of TM4 (N2.52 182 and Y3.52 250 ) that also influence cell signalling. Collectively, this work expands our understanding of peptide-mediated signalling by the GLP-1 receptor. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Two-micrometer thulium laser resection of the prostate-tangerine technique in benign prostatic hyperplasia patients with previously negative transrectal prostate biopsy.

PubMed

Zhuo, Jian; Wei, Hai-Bin; Zhang, Fei; Liu, Hai-Tao; Zhao, Fu-Jun; Han, Bang-Min; Sun, Xiao-Wen; Xia, Shu-Jie

2017-01-01

The 2-μm thulium laser resection of the prostate-tangerine technique (TmLRP-TT) has been introduced as a minimally invasive treatment for benign prostatic hyperplasia (BPH). This study was undertaken to assess the clinical efficacy and safety of TmLRP-TT for the treatment of BPH patients with previously negative transrectal prostate biopsy. A prospective analysis of 51 patients with previously negative transrectal prostate biopsy who underwent surgical treatment using TmLRP-TT was performed from December 2011 to December 2013. Preoperative status, surgical details, and perioperative complications were recorded. The follow-up outcome was evaluated with subjective and objective tests at 1 and 6 months. TmLRP-TT was successfully completed in all patients. Mean prostate volume, operative duration, and catheterization time were 93.3 ± 37.9 ml, 69.5 ± 39.5 min, and 6.5 ± 1.3 days, respectively. The mean International Prostate Symptom Score, quality of life score, maximum urinary flow rate, and post-void residual urine volume changed notably at 6-month follow-up (22.5 ± 6.9 vs 6.1 ± 3.2, 4.8 ± 1.3 vs 1.1 ± 0.9, 7.3 ± 4.5 vs 18.9 ± 7.1 ml s-1 , and 148.7 ± 168.7 vs 28.4 ± 17.9 ml). Two (3.9%) patients required blood transfusion perioperatively, while 3 (5.9%) patients experienced transient hematuria postoperatively, and 2 (3.9%) patients received 3 days recatheterization due to clot retention. TmLRP-TT is a safe and effective minimally invasive technique for patients with previously negative transrectal prostate biopsy during the 6-month follow-up. This promising technology may be a feasible surgical method for previously negative transrectal prostate biopsy in the future.

Two-micrometer thulium laser resection of the prostate-tangerine technique in benign prostatic hyperplasia patients with previously negative transrectal prostate biopsy

PubMed Central

Zhuo, Jian; Wei, Hai-Bin; Zhang, Fei; Liu, Hai-Tao; Zhao, Fu-Jun; Han, Bang-Min; Sun, Xiao-Wen; Jun-Lu; Xia, Shu-Jie

2017-01-01

The 2-μm thulium laser resection of the prostate-tangerine technique (TmLRP-TT) has been introduced as a minimally invasive treatment for benign prostatic hyperplasia (BPH). This study was undertaken to assess the clinical efficacy and safety of TmLRP-TT for the treatment of BPH patients with previously negative transrectal prostate biopsy. A prospective analysis of 51 patients with previously negative transrectal prostate biopsy who underwent surgical treatment using TmLRP-TT was performed from December 2011 to December 2013. Preoperative status, surgical details, and perioperative complications were recorded. The follow-up outcome was evaluated with subjective and objective tests at 1 and 6 months. TmLRP-TT was successfully completed in all patients. Mean prostate volume, operative duration, and catheterization time were 93.3 ± 37.9 ml, 69.5 ± 39.5 min, and 6.5 ± 1.3 days, respectively. The mean International Prostate Symptom Score, quality of life score, maximum urinary flow rate, and post-void residual urine volume changed notably at 6-month follow-up (22.5 ± 6.9 vs 6.1 ± 3.2, 4.8 ± 1.3 vs 1.1 ± 0.9, 7.3 ± 4.5 vs 18.9 ± 7.1 ml s−1, and 148.7 ± 168.7 vs 28.4 ± 17.9 ml). Two (3.9%) patients required blood transfusion perioperatively, while 3 (5.9%) patients experienced transient hematuria postoperatively, and 2 (3.9%) patients received 3 days recatheterization due to clot retention. TmLRP-TT is a safe and effective minimally invasive technique for patients with previously negative transrectal prostate biopsy during the 6-month follow-up. This promising technology may be a feasible surgical method for previously negative transrectal prostate biopsy in the future. PMID:26732107

Investigating vegetation spectral reflectance for detecting hydrocarbon pipeline leaks from multispectral data

NASA Astrophysics Data System (ADS)

Adamu, Bashir; Tansey, Kevin; Bradshaw, Michael J.

2013-10-01

The aim of this paper is to analyse spectral reflectance data from Landsat TM of vegetation that has been exposed to hydrocarbon contamination from oil spills from pipelines. The study is undertaken in an area of mangrove and swamp vegetation where the detection of an oil spill is traditionally difficult to make. We used a database of oil spill records to help identify candidate sites for spectral analysis. Extracted vegetation spectra were compared between polluted and nonpolluted sites and supervised (neural network) classification was carried out to map hydrocarbon (HC) contaminated sites from the sample areas. Initial results show that polluted sites are characterised by high reflectance in the visible (VIS) 0.4μm - 0.7μm, and a lower reflectance in the near-infrared (NIR) 0.7μm - 1.1μm. This suggests that the vegetation is in a stressed state. Samples taken from pixels surrounding polluted sites show similar spectral reflectance values to that of polluted sites suggesting possible migration of HC to the wider environment. Further work will focus on increasing the sample size and investigating the impact of an oil spill on a wider buffer zone around the spill site.

Structural modulation of gut microbiota in Bama minipigs in response to treatment with a "growth-promoting agent", salbutamol.

PubMed

Lu, Chenyang; Zhou, Jun; Li, Yanyan; Zhang, Dijun; Wang, Zuzhong; Li, Ye; Cheong, Lingzhi; Zhang, Chundan; Su, Xiurong

2017-07-01

Even though salbutamol (SAL) had remarkable effects on the enhancement of growth rate and carcass composition in different livestock species such as cattle, pigs, sheep and poultry, it was banned as a growth promoter because of its adverse effects on health. However, the specific mechanism by which salbutamol enhances growth efficiency remains unknown. In this study, Bama pigs were randomly allocated to receive salbutamol (5 mg/kg) for 30 or 60 days and were compared with untreated pigs. Pigs treated with salbutamol demonstrated enhanced growth rates and carcass composition; however, they showed deterioration in blood biochemical indices and organ development. We hypothesized that salbutamol exerts its effects by modulating the composition of the gut microbiota population. The faecal microbiome of pigs was characterized via pyrosequencing of the bacterial 16S rRNA gene. The gut microbiota population analysis showed that salbutamol caused shifts in the microbial composition of less abundant species. Redundancy analysis indicated an increase in abundance of the phylum Bacteroidetes, class Betaproteobacteria, family Christensenellaceae and genus Lactobacillus, and a decreased ratio of the phylum Firmicutes, class Clostridia and genera Ruminococcus, Blautia and Subdoligranulum. In conclusion, our study provided circumstantial evidence that the various effects of salbutamol are caused by gut microbiota modulation, and several potential candidates were identified for SAL detection via the gut microbiota. Our findings provided new insights into the roles of the gut microbiota during salbutamol treatment, and these findings will aid in the screening of alternative strategies for animal health improvement and production enhancement.

Bacterial community shift during the startup of a full-scale oxidation ditch treating sewage.

PubMed

Chen, Yajun; Ye, Lin; Zhao, Fuzheng; Xiao, Lin; Cheng, Shupei; Zhang, Xu-Xiang

2016-10-06

Oxidation ditch (OD) is one of the most widely used processes for treating municipal wastewater. However, the microbial communities in the OD systems have not been well characterized and little information about the shift of bacterial community during the startup process of the OD systems is available. In this study, we investigated the bacterial community changes during the startup period (over 100 days) of a full-scale OD. The results showed that the bacterial community dramatically changed during the startup period. Similar to the activated sludge samples in other studies, Proteobacteria (accounting for 26.3%~48.4%) was the most dominant bacterial phylum in the OD system but its relative abundance declined nearly 40% during the startup process. It was also found that Planctomycetes proliferated greatly (from 4.79% to 13.5%) and finally replaced Bacteroidetes as the second abundant phylum in the OD system. Specifically, some bacteria affiliated with Flavobacterium genus of exhibited remarkable decreasing trends, while bacterial species belonging to OD1 candidate division and Saprospiraceae family were found to increase during the startup process. Despite of the bacterial community shift, the organic matter, nitrogen and phosphorus in the effluent were always in low concentrations, suggesting the functional redundancy of the bacterial community. Moreover, by comparing with the bacterial community in other municipal wastewater treatment bioreactors, some potentially novel bacterial species were found to be present in the OD system. Collectively, this study improved our understandings of bacterial community structure and the microbial ecology during the startup of full-scale wastewater treatment bioreactor.

Mechanical damage of tympanic membrane in relation to impulse pressure waveform - A study in chinchillas.

PubMed

Gan, Rong Z; Nakmali, Don; Ji, Xiao D; Leckness, Kegan; Yokell, Zachary

2016-10-01

Mechanical damage to middle ear components in blast exposure directly causes hearing loss, and the rupture of the tympanic membrane (TM) is the most frequent injury of the ear. However, it is unclear how the severity of injury graded by different patterns of TM rupture is related to the overpressure waveforms induced by blast waves. In the present study, the relationship between the TM rupture threshold and the impulse or overpressure waveform has been investigated in chinchillas. Two groups of animals were exposed to blast overpressure simulated in our lab under two conditions: open field and shielded with a stainless steel cup covering the animal head. Auditory brainstem response (ABR) and wideband tympanometry were measured before and after exposure to check the hearing threshold and middle ear function. Results show that waveforms recorded in the shielded case were different from those in the open field and the TM rupture threshold in the shielded case was lower than that in the open field (3.4 ± 0.7 vs. 9.1 ± 1.7 psi or 181 ± 1.6 vs. 190 ± 1.9 dB SPL). The impulse pressure energy spectra analysis of waveforms demonstrates that the shielded waveforms include greater energy at high frequencies than that of the open field waves. Finally, a 3D finite element (FE) model of the chinchilla ear was used to compute the distributions of stress in the TM and the TM displacement with impulse pressure waves. The FE model-derived change of stress in response to pressure loading in the shielded case was substantially faster than that in the open case. This finding provides the biomechanical mechanisms for blast induced TM damage in relation to overpressure waveforms. The TM rupture threshold difference between the open and shielded cases suggests that an acoustic role of helmets may exist, intensifying ear injury during blast exposure. Copyright © 2016 Elsevier B.V. All rights reserved.

Validation of the firefighter WFI treadmill protocol for predicting VO2 max.

PubMed

Dolezal, B A; Barr, D; Boland, D M; Smith, D L; Cooper, C B

2015-03-01

The Wellness-Fitness Initiative submaximal treadmill exercise test (WFI-TM) is recommended by the US National Fire Protection Agency to assess aerobic capacity (VO2 max) in firefighters. However, predicting VO2 max from submaximal tests can result in errors leading to erroneous conclusions about fitness. To investigate the level of agreement between VO2 max predicted from the WFI-TM against its direct measurement using exhaled gas analysis. The WFI-TM was performed to volitional fatigue. Differences between estimated VO2 max (derived from the WFI-TM equation) and direct measurement (exhaled gas analysis) were compared by paired t-test and agreement was determined using Pearson Product-Moment correlation and Bland-Altman analysis. Statistical significance was set at P < 0.05. Fifty-nine men performed the WFI-TM. Mean (standard deviation) values for estimated and measured VO2 max were 44.6 (3.4) and 43.6 (7.9) ml/kg/min, respectively (P < 0.01). The mean bias by which WFI-TM overestimated VO2 max was 0.9ml/kg/min with a 95% prediction interval of ±13.1. Prediction errors for 22% of subjects were within ±5%; 36% had errors greater than or equal to ±15% and 7% had greater than ±30% errors. The correlation between predicted and measured VO2 max was r = 0.55 (standard error of the estimate = 2.8ml/kg/min). WFI-TM predicts VO2 max with 11% error. There is a tendency to overestimate aerobic capacity in less fit individuals and to underestimate it in more fit individuals leading to a clustering of values around 42ml/kg/min, a criterion used by some fire departments to assess fitness for duty. © The Author 2015. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment.

PubMed

Imachi, Hiroyuki; Sakai, Sanae; Lipp, Julius S; Miyazaki, Masayuki; Saito, Yumi; Yamanaka, Yuko; Hinrichs, Kai-Uwe; Inagaki, Fumio; Takai, Ken

2014-03-01

A novel, anaerobic filamentous bacterium, strain MO-CFX1(T), was isolated from a methanogenic community, which was originally established from subseafloor sediments collected from off the Shimokita Peninsula, Japan. Cells were non-spore-forming, non-motile, Gram-stain-negative and filamentous. The filaments were longer than 10 µm and 130-150 nm in width. Growth of the strain was observed at 10-37 °C (optimum 25-30 °C), at pH 5.5-8.5 (optimum pH 7.0) and in 0-50 g NaCl l(-1) (optimum 15 g NaCl l(-1)). The strain was able to grow with a number of carbohydrates in the presence of yeast extract. The major cellular fatty acids were monounsaturated C18 : 1ω9, C16 : 1ω7 and saturated C18 : 0 and C16 : 0. The intact polar lipids of the strain were dominated by diacylglyceride and sphingolipid core lipid structures with monoglycosidic, mixed phosphomonoglycosidic and fatty-acid-modified monoglycosidic polar head groups. The G+C content of the genomic DNA was 52.4 mol%. Based on the comparative 16S rRNA gene sequence analysis, strain MO-CFX1(T) was affiliated with the class Anaerolineae within the phylum Chloroflexi and was most closely related to Leptolinea tardivitalis YMTK-2(T) (sequence identity of 91.0 %). Based on phenotypic and genetic properties of the novel isolate, we propose a novel species representing a new genus Pelolinea submarina gen. nov., sp. nov., for strain MO-CFX1(T) ( = JCM 17238(T), = KCTC 5975(T)). This is the first formal description, to our knowledge, of an isolate of the phylum Chloroflexi from the deep-sea sedimentary environment.

Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem.

PubMed

Suzuki, Shino; Ishii, Shun'ichi; Wu, Angela; Cheung, Andrea; Tenney, Aaron; Wanger, Greg; Kuenen, J Gijs; Nealson, Kenneth H

2013-09-17

The Cedars, in coastal northern California, is an active site of peridotite serpentinization. The spring waters that emerge from this system feature very high pH, low redox potential, and low ionic concentrations, making it an exceptionally challenging environment for life. We report a multiyear, culture-independent geomicrobiological study of three springs at The Cedars that differ with respect to the nature of the groundwater feeding them. Within each spring, both geochemical properties and microbial diversity in all three domains of life remained stable over a 3-y period, with multiple samples each year. Between the three springs, however, the microbial communities showed considerable differences that were strongly correlated with the source of the serpentinizing groundwater. In the spring fed solely by deep groundwater, phylum Chloroflexi, class Clostridia, and candidate division OD1 were the major taxa with one phylotype in Euryarchaeota. Less-abundant phylotypes include several minor members from other candidate divisions and one phylotype that was an outlier of candidate division OP3. In the springs fed by the mixture of deep and shallow groundwater, organisms close to the Hydrogenophaga within Betaproteobacteria dominated and coexisted with the deep groundwater community members. The shallow groundwater community thus appears to be similar to those described in other terrestrial serpentinizing sites, whereas the deep community is distinctly different from any other previously described terrestrial serpentinizing community. These unique communities have the potential to yield important insights into the development and survival of life in these early-earth analog environments.

Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem

PubMed Central

Suzuki, Shino; Ishii, Shun’ichi; Wu, Angela; Cheung, Andrea; Tenney, Aaron; Wanger, Greg; Kuenen, J. Gijs; Nealson, Kenneth H.

2013-01-01

The Cedars, in coastal northern California, is an active site of peridotite serpentinization. The spring waters that emerge from this system feature very high pH, low redox potential, and low ionic concentrations, making it an exceptionally challenging environment for life. We report a multiyear, culture-independent geomicrobiological study of three springs at The Cedars that differ with respect to the nature of the groundwater feeding them. Within each spring, both geochemical properties and microbial diversity in all three domains of life remained stable over a 3-y period, with multiple samples each year. Between the three springs, however, the microbial communities showed considerable differences that were strongly correlated with the source of the serpentinizing groundwater. In the spring fed solely by deep groundwater, phylum Chloroflexi, class Clostridia, and candidate division OD1 were the major taxa with one phylotype in Euryarchaeota. Less-abundant phylotypes include several minor members from other candidate divisions and one phylotype that was an outlier of candidate division OP3. In the springs fed by the mixture of deep and shallow groundwater, organisms close to the Hydrogenophaga within Betaproteobacteria dominated and coexisted with the deep groundwater community members. The shallow groundwater community thus appears to be similar to those described in other terrestrial serpentinizing sites, whereas the deep community is distinctly different from any other previously described terrestrial serpentinizing community. These unique communities have the potential to yield important insights into the development and survival of life in these early-earth analog environments. PMID:24003156

Intra-annual NDVI validation of the Landsat 5 TM radiometric calibration

USGS Publications Warehouse

Chander, G.; Groeneveld, D.P.

2009-01-01

Multispectral data from the Landsat 5 (L5) Thematic Mapper (TM) sensor provide the backbone of the extensive archive of moderate‐resolution Earth imagery. Even after more than 24 years of service, the L5 TM is still operational. Given the longevity of the satellite, the detectors have aged and the sensor's radiometric characteristics have changed since launch. The calibration procedures and parameters in the National Land Archive Production System (NLAPS) have also changed with time. Revised radiometric calibrations in 2003 and 2007 have improved the radiometric accuracy of recently processed data. This letter uses the Normalized Difference Vegetation Index (NDVI) as a metric to evaluate the radiometric calibration. The calibration change has improved absolute calibration accuracy, consistency over time, and consistency with Landsat 7 (L7) Enhanced Thematic radiometry and will provide the basis for continued long‐term studies of the Earth's land surfaces.

Comparison of rectal, tympanic membrane and axillary temperature measurement methods in dogs.

PubMed

Lamb, V; McBrearty, A R

2013-11-30

The aim of this study was to compare axillary and tympanic membrane (TM) temperature measurements to rectal temperature in a large group of clinical canine patients. We also sought to ascertain whether certain factors affected the differences between the measurements and to compare the ease of measurement. Axillary temperatures were easy to obtain but tended to be lower than rectal readings (median difference 0.6°C). In 54.7 per cent of dogs there was a difference of >0.5°C between the two readings. Weight, coat length, body condition score and breed size were significantly associated with the difference between the rectal and axillary temperature. TM temperatures were more similar to rectal temperatures (median difference 0°C) but in 25 per cent of dogs, there was a difference of >0.5°C between rectal and TM readings. TM measurements were less well tolerated than axillary measurements. None of the factors assessed were associated with the difference between the rectal and TM temperature. As a difference of >0.5°C has previously been described as unacceptable for different methods of temperature measurement, neither axillary nor TM temperatures are interchangeable with rectal temperatures for the measurement of body temperature.

The prevalence and spectrum of sleep problems in women with transformed migraine.

PubMed

Calhoun, Anne H; Ford, Sutapa; Finkel, Alan G; Kahn, Kevin A; Mann, J Douglas

2006-04-01

It is our clinical observation that patients with transformed migraine (TM) almost invariably report nonrestorative sleep. In this study we sought first to validate that clinical observation, then to describe the prevalence and spectrum of factors that might contribute to nonrestorative sleep in a TM population. Although headaches have been linked with sleep problems for over a century, there is little information about the spectrum or prevalence of specific sleep problems associated with TM in adults. We conducted a detailed sleep interview on 147 consecutive women with TM. Subjective sleep quality was assessed by asking patients to describe their state upon awakening as "refreshed" or "tired." None of the 147 patients reported awakening "refreshed," and 83.7% stated that they awakened "tired." Sleep complaints were prevalent and varied in this population. Although the relationship between pain and sleep is complex and ill understood, we found a very high prevalence of nonrestorative sleep and a similarly high prevalence of modifiable poor sleep habits in patients with TM. Since behavioral approaches have been found effective in improving sleep quality in patients with poor sleep hygiene, we propose that studies be undertaken to assess the impact of such treatment on TM.

Evaluation of corn/soybeans separability using Thematic Mapper and Thematic Mapper Simulator data

NASA Technical Reports Server (NTRS)

Pitts, D. E.; Badhwar, G. D.; Thompson, D. R.; Henderson, K. E.; Shen, S. S.; Sorensen, C. T.; Carnes, J. G.

1984-01-01

Multitemporal Thematic Mapper, Thematic Mapper Simulator, and detailed ground truth data were collected for a 9- by 11-km sample segment in Webster County, IA, in the summer of 1982. Three dates were acquired each with Thematic Mapper Simulator (June 7, June 23, and July 31) and Thematic Mapper (August 2, September 3, and October 21). The Thematic Mapper Simulator data were converted to equivalent TM count values using TM and TMS calibration data and model based estimates of atmospheric effects. The July 31, TMS image was compared to the August 2, TM image to verify the conversion process. A quantitative measure of proportion estimation variance (Fisher information) was used to evaluate the corn/soybeans separability for each TM band as a function of time during the growing season. The additional bands in the middle infrared allowed corn and soybeans to be separated much earlier than was possible with the visible and near-infrared bands alone. Using the TM and TMS data, temporal profiles of the TM principal components were developed. The greenness and brightness exhibited behavior similar to MSS greenness and brightness for corn and soybeans.

Global Diversity of the Placozoa

PubMed Central

Eitel, Michael; Osigus, Hans-Jürgen; DeSalle, Rob; Schierwater, Bernd

2013-01-01

The enigmatic animal phylum Placozoa holds a key position in the metazoan Tree of Life. A simple bauplan makes it appear to be the most basal metazoan known and genetic evidence also points to a position close to the last common metazoan ancestor. Trichoplax adhaerens is the only formally described species in the phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molecular genetic as well as morphological studies have identified a high level of diversity, and hence a potential high level of taxonomic diversity, within this phylum. Different taxa, possibly at different taxonomic levels, are awaiting description. In this review we firstly summarize knowledge on the morphology, phylogenetic position and ecology of the Placozoa. Secondly, we give an overview of placozoan morphological and genetic diversity and finally present an updated distribution of placozoan populations. We conclude that there is great potential and need to erect new taxa and to establish a firm system for this taxonomic tabula rasa. PMID:23565136

MRI-guided tumor tracking in lung cancer radiotherapy

NASA Astrophysics Data System (ADS)

Cerviño, Laura I.; Du, Jiang; Jiang, Steve B.

2011-07-01

Precise tracking of lung tumor motion during treatment delivery still represents a challenge in radiation therapy. Prototypes of MRI-linac hybrid systems are being created which have the potential of ionization-free real-time imaging of the tumor. This study evaluates the performance of lung tumor tracking algorithms in cine-MRI sagittal images from five healthy volunteers. Visible vascular structures were used as targets. Volunteers performed several series of regular and irregular breathing. Two tracking algorithms were implemented and evaluated: a template matching (TM) algorithm in combination with surrogate tracking using the diaphragm (surrogate was used when the maximum correlation between the template and the image in the search window was less than specified), and an artificial neural network (ANN) model based on the principal components of a region of interest that encompasses the target motion. The mean tracking error ē and the error at 95% confidence level e95 were evaluated for each model. The ANN model led to ē = 1.5 mm and e95 = 4.2 mm, while TM led to ē = 0.6 mm and e95 = 1.0 mm. An extra series was considered separately to evaluate the benefit of using surrogate tracking in combination with TM when target out-of-plane motion occurs. For this series, the mean error was 7.2 mm using only TM and 1.7 mm when the surrogate was used in combination with TM. Results show that, as opposed to tracking with other imaging modalities, ANN does not perform well in MR-guided tracking. TM, however, leads to highly accurate tracking. Out-of-plane motion could be addressed by surrogate tracking using the diaphragm, which can be easily identified in the images.

76 FR 3046 - Farmers' Market Promotion Program Regulation; Notice of Request for Approval of a New Information...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-19

... Service 7 CFR Part 185 [Document No. AMS-TM-10-0088; TM-08-07] RIN 0581-AC83 Farmers' Market Promotion... Promotion Program (FMPP). The FMPP is a competitive grant program that makes funds available to eligible... information collection OMB 0581-0235, entitled Farmers' Market Promotion Program. DATES: Comments received by...

Polyimide Composites from 'Salt-Like' Solution Precursors

NASA Technical Reports Server (NTRS)

Cano, Roberto J.; Hou, Tan H.; Weiser, Erik S.; SaintClair, Terry L.

2001-01-01

Four NASA Langley-developed polyimide matrix resins, LaRC(TM)-IA, LaRC(TM)-IAX, LaRC(TM)-8515 and LaRC(TM)-PETI-5, were produced via a 'saltlike' process developed by Unitika Ltd. The salt-like solutions (65% solids in NMP) were prepregged onto Hexcel IM7 carbon fiber using the NASA LaRC multipurpose tape machine. Process parameters were determined and composite panels fabricated. The temperature dependent volatile depletion rates, the thermal crystallization behavior and the resin rheology were characterized. Composite molding cycles were developed which consistently yielded well consolidated, void-free laminated parts. Composite mechanical properties such as the short beam shear strength; the longitudinal and transverse flexural strength and flexural modulus; the longitudinal compression strength and modulus; and the open hole compression strength and compression after impact strength were measured at room temperature and elevated temperatures. The processing characteristics and the composite mechanical properties of the four intermediate modulus carbon fiber/polyimide matrix composites were compared to existing data on the same polyimide resin systems and IM7 carbon fiber manufactured via poly(amide acid) solutions (30-35% solids in NMP). This work studies the effects of varying the synthetic route on the processing and mechanical properties of the polyimide composites.

Data compression experiments with LANDSAT thematic mapper and Nimbus-7 coastal zone color scanner data

NASA Technical Reports Server (NTRS)

Tilton, James C.; Ramapriyan, H. K.

1989-01-01

A case study is presented where an image segmentation based compression technique is applied to LANDSAT Thematic Mapper (TM) and Nimbus-7 Coastal Zone Color Scanner (CZCS) data. The compression technique, called Spatially Constrained Clustering (SCC), can be regarded as an adaptive vector quantization approach. The SCC can be applied to either single or multiple spectral bands of image data. The segmented image resulting from SCC is encoded in small rectangular blocks, with the codebook varying from block to block. Lossless compression potential (LDP) of sample TM and CZCS images are evaluated. For the TM test image, the LCP is 2.79. For the CZCS test image the LCP is 1.89, even though when only a cloud-free section of the image is considered the LCP increases to 3.48. Examples of compressed images are shown at several compression ratios ranging from 4 to 15. In the case of TM data, the compressed data are classified using the Bayes' classifier. The results show an improvement in the similarity between the classification results and ground truth when compressed data are used, thus showing that compression is, in fact, a useful first step in the analysis.

Multiparametric ultrasonography and ultrasound elastography in the differentiation of parathyroid lesions from ectopic thyroid lesions or lymphadenopathies.

PubMed

Isidori, Andrea M; Cantisani, Vito; Giannetta, Elisa; Diacinti, Daniele; David, Emanuele; Forte, Valerio; Elia, Daniela; De Vito, Corrado; Sbardella, Emilia; Gianfrilli, Daniele; Monteleone, Francesco; Pepe, Jessica; Minisola, Salvatore; Ascenti, Giorgio; D'Andrea, Vito; Catalano, Carlo; D'Ambrosio, Ferdinando

2017-08-01

To evaluate the accuracy of ultrasound elastography with Elastoscan TM Core Index in the differential diagnosis of parathyroid lesions from ectopic thyroid nodules and lymph nodes. Seventy nine patients with repeatedly high levels of circulating intact parathyroid hormone, normal vitamin D and renal function tests, with an ultrasound scan showing a neck lesion, sharply demarcated from the thyroid lobules, were consecutively enrolled. Ultrasound with and without Color Doppler and ultrasound elastography were performed before histological examination. All ultrasound features, vascularization and ultrasound elastography diagnostic performance were assessed using ROC curves. Histological examination confirmed 47 parathyroid lesions, 18 thyroid ectopic nodules and 14 reactive lymph nodes. In distinguishing parathyroid from thyroid nodules, shape had a 100 % sensitivity (95 % CI 92.4-100) and 50 % specificity (95 % CI 37.2-64.7), cleavage had a 85.1 % sensitivity (95 % CI 72.3-92.6) and 77.8 % specificity (95 % CI 65.1-88) while peripheral vascularization had a sensitivity of 91.5 (95 % CI 79.6-97.6) and specificity of 72.2 (95 % CI 46.5-90.3). An Elastoscan TM Core Indexof 1.28 was 46 % sensitive (95 % CI 33.4-58.7) and 77 % specific (95 % CI 66.2-89.1) in discriminating parathyroid lesions from thyroid nodules. An Elastoscan TM Core Index of 1.0 was 78 % sensitive (95 % CI 65.1-88) and 71 % specific (95 % CI 56-81.3) in discriminating parathyroid lesions from lymph nodes (p = 0.045). An Elastoscan TM Core Index greater than 2.58 had a 100 % sensitivity (95 % CI 43.8-100) and 95.4 % specificity (95 % CI 38.3-99.7) in discriminating malignant from benign parathyroid nodules. Elastoscan TM Core Index was significantly higher in thyroid nodules than in reactive lymph nodes (1.18 ± 0.62, p = 0.008). The ultrasound features of cleavage and peripheral vascularization help to differentiate parathyroid from thyroid nodules. Elastoscan TM Core Index can improve ultrasound discrimination of parathyroid lesions from lymph nodes. The Elastoscan TM Core Index is significantly higher in malignant than in benign parathyroid lesions.

Teriyaki sauce with carvacrol or thymol effectively controls Escherichia coli O157:H7, Listeria monocytogenes, Salmonella Typhimurium, and indigenous flora in marinated beef and marinade.

PubMed

Moon, Hyeree; Kim, Nam Hee; Kim, Soon Han; Kim, Younghoon; Ryu, Jee Hoon; Rhee, Min Suk

2017-07-01

An effective bactericidal cold-marinating method for beef products is described, exploiting the synergism between soy sauce and natural compounds (carvacrol, CV or thymol, TM) to reduce microbiological risks. Beef slices inoculated with Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium (3.1-3.5logCFU/g) were marinated in a teriyaki sauce with or without CV and TM (0.3 and 0.5%). After 1, 3, and 7days at 4°C, indigenous microflora population, color, lipid oxidation, marinade uptake, and pH of marinated beef and leftover marinade samples were examined. Teriyaki sauce alone did not reduce or inhibit any of the target pathogens or indigenous bacteria, while 0.5% CV- or TM-containing teriyaki sauce inactivated all inocula without recovery within 7days (p<0.05). The pathogens relocated from the beef into the leftover marinade (3.0-3.4logCFU/mL) were also completely inactivated. The treatment inhibited growth of indigenous aerobic bacteria (p<0.05) and inactivated coliform bacteria. Physicochemical parameters were not significantly affected (p>0.05). Copyright © 2017 Elsevier Ltd. All rights reserved.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

PubMed Central

Badhai, Jhasketan; Ghosh, Tarini S.; Das, Subrata K.

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria. PMID:26579081

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany).

PubMed

Röske, Kerstin; Sachse, René; Scheerer, Carola; Röske, Isolde

2012-02-01

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity (H') ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites. Copyright © 2011 Elsevier GmbH. All rights reserved.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

PubMed

Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Analysis of conifer forest regeneration using Landsat Thematic Mapper data

NASA Technical Reports Server (NTRS)

Fiorella, Maria; Ripple, William J.

1995-01-01

Landsat Thematic Mapper (TM) data were used to evaluate young conifer stands in the western Cascade Mountains of Oregon. Regression and correlation analyses were used to describe the relationships between TM band values and age of young Douglas-fir stands (2 to 35 years old). Spectral data from well regenerated Douglas-fir stands were compared to those of poorly regenerated conifer stands. TM bands 1, 2, 3, 5, 6, and 7 were inversely correlated with the age (r greater than or equal to -0.80) of well regenerated Douglas-fir stands. Overall, the 'structural index' (TM 4/5 ratio) had the highest correlation to age of Douglas-fir stands (r = 0.96). Poorly regenerated stands were spectrally distinct from well regenerated Douglas-fir stands after the stands reached an age of approximately 15 years.

Spectral reflectance of surface soils - A statistical analysis

NASA Technical Reports Server (NTRS)

Crouse, K. R.; Henninger, D. L.; Thompson, D. R.

1983-01-01

The relationship of the physical and chemical properties of soils to their spectral reflectance as measured at six wavebands of Thematic Mapper (TM) aboard NASA's Landsat-4 satellite was examined. The results of performing regressions of over 20 soil properties on the six TM bands indicated that organic matter, water, clay, cation exchange capacity, and calcium were the properties most readily predicted from TM data. The middle infrared bands, bands 5 and 7, were the best bands for predicting soil properties, and the near infrared band, band 4, was nearly as good. Clustering 234 soil samples on the TM bands and characterizing the clusters on the basis of soil properties revealed several clear relationships between properties and reflectance. Discriminant analysis found organic matter, fine sand, base saturation, sand, extractable acidity, and water to be significant in discriminating among clusters.

High beam quality of a Q-switched 2-µm Tm,Ho:LuVO4 laser

NASA Astrophysics Data System (ADS)

Wang, Wei; Yang, Xining; Shen, Yingjie; Li, Linjun; Zhou, Long; Yang, Yuqiang; Bai, Yunfeng; Xie, Wenqiang; Ye, Guangchao; Yu, Xiaoyang

2018-05-01

A diode-end-pumped 2.05-µm Q-switched Tm,Ho:LuVO4 laser is reported in this paper. The cryogenic Tm3+ (5.0 at.%),Ho3+ (0.5 at.%):LuVO4 crystal was pumped by an 800-nm laser diode. At a pulse repetition frequency of 10 kHz, the maximum average output power of 3.77 W was achieved at 77 K when an incident pump power of 14.7 W was used. The slope efficiency and optical-optical conversion efficiency were 28.3 and 25.6%, respectively. The maximum per pulse energy was 2.54 mJ for a pulse duration of 69.9 ns. The beam quality factor Mx 2 was approximately 1.17 and My 2 was approximately 1.01 for the Tm,Ho:LuVO4 laser.

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

USDA-ARS?s Scientific Manuscript database

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few gen...

[Influence of tobacco-Chuanminshen violaceum rotation on microbe community in soil].

PubMed

Zhang, Dong-Yan; Zhao, Jian; Yang, Shui-Ping; Mo, Jing-Jing; He, Da-Min; Wang, Jun; Gou, Jian-Yu; Zhang, Xue; Jiang, Wei; Wen, Ming-Xia

2016-12-01

Soil microbes are the important indicator of soil quality. For exploring Chuanminshen violaceum planting to microbial effects in tobacco soil, this paper adopted Illumina MiSeq high-throughput sequencing to research the change of bacteria and fungi at the phylum and genus in the soil. The results showed that the Ch. violaceum planting increased the biodiversity of bacteria and fungi. The influence on fungi was greater than that on bacteria. It greatly increased the sequence of fungi, it obtained 32 978 16S rDNA and 32 229 18S rDNA sequence number. There was no change of the top three phylums in bacteria, but the content changed, Proteobacteria and Acidobacteria reduced by 1.73% and 1.4% respectively, and Actinobacteria increased by 0.65%. The advantage phylum Ascomycete in tobacco reduced by 27.99% to be second advantage phylum after Ch. violaceum planting, and the second advantage phylum Basidiomycete increased by 23.69% to become the first dominant fungi. At the genus, Ch. violaceum planting changed the order of dominant genus and the abundance was also changed. Some changed largely such as uncultured Acidobacteriaceae Subgroup-1, Gemmatimonas, Subgroup-2,uncultured Nitrosomonadaceae for bacteria, norank Sordariales, norank Agaricomycetes, Phialophora for fungi. Especially the rotation increased antagonistic microbes and physiological microbes and decreased pathogenic microbes. So the Ch. violaceum planting can improve the microbe community in tobacco soil. Copyright© by the Chinese Pharmaceutical Association.

RNA interference can be used to disrupt gene function in tardigrades

PubMed Central

Tenlen, Jennifer R.; McCaskill, Shaina; Goldstein, Bob

2012-01-01

How morphological diversity arises is a key question in evolutionary developmental biology. As a long-term approach to address this question, we are developing the water bear Hypsibius dujardini (Phylum Tardigrada) as a model system. We expect that using a close relative of two well-studied models, Drosophila (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda), will facilitate identifying genetic pathways relevant to understanding the evolution of development. Tardigrades are also valuable research subjects for investigating how organisms and biological materials can survive extreme conditions. Methods to disrupt gene activity are essential to each of these efforts, but no such method yet exists for the Phylum Tardigrada. We developed a protocol to disrupt tardigrade gene functions by double-stranded RNA-mediated RNA interference (RNAi). We show that targeting tardigrade homologs of essential developmental genes by RNAi produced embryonic lethality, whereas targeting green fluorescent protein did not. Disruption of gene functions appears to be relatively specific by two criteria: targeting distinct genes resulted in distinct phenotypes that were consistent with predicted gene functions, and by RT-PCR, RNAi reduced the level of a target mRNA and not a control mRNA. These studies represent the first evidence that gene functions can be disrupted by RNAi in the phylum Tardigrada. Our results form a platform for dissecting tardigrade gene functions for understanding the evolution of developmental mechanisms and survival in extreme environments. PMID:23187800

RNA interference can be used to disrupt gene function in tardigrades.

PubMed

Tenlen, Jennifer R; McCaskill, Shaina; Goldstein, Bob

2013-05-01

How morphological diversity arises is a key question in evolutionary developmental biology. As a long-term approach to address this question, we are developing the water bear Hypsibius dujardini (Phylum Tardigrada) as a model system. We expect that using a close relative of two well-studied models, Drosophila (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda), will facilitate identifying genetic pathways relevant to understanding the evolution of development. Tardigrades are also valuable research subjects for investigating how organisms and biological materials can survive extreme conditions. Methods to disrupt gene activity are essential to each of these efforts, but no such method yet exists for the Phylum Tardigrada. We developed a protocol to disrupt tardigrade gene functions by double-stranded RNA-mediated RNA interference (RNAi). We showed that targeting tardigrade homologs of essential developmental genes by RNAi produced embryonic lethality, whereas targeting green fluorescent protein did not. Disruption of gene functions appears to be relatively specific by two criteria: targeting distinct genes resulted in distinct phenotypes that were consistent with predicted gene functions and by RT-PCR, RNAi reduced the level of a target mRNA and not a control mRNA. These studies represent the first evidence that gene functions can be disrupted by RNAi in the phylum Tardigrada. Our results form a platform for dissecting tardigrade gene functions for understanding the evolution of developmental mechanisms and survival in extreme environments.

The suitability of different probiotic strains for the production of fruit-whey beverages.

PubMed

Sady, Marek; Najgebauer-Lejko, Dorota; Domagała, Jacek

2017-01-01

When designing new probiotic products, one of the most important aspects is the selection of bacterial strains with high survival rates in the matrix of the product concerned. The aim of the present research was to evaluate the potential of selected strains of probiotic bacteria for the production of fruit-whey beverages. Orange, apple and blackcurrant whey beverages were produced, and each was inoculated with one of the following probiotic strains: Bifidobacterium lactis HN019TM; Lactobacillus aci- dophilus NCFM®; Lactobacillus paracasei Lpc-37TM; Lactobacillus rhamnosus HN001TM. The count of probiotic bacteria as well as pH and total acidity were evaluated at the 1st, 7th, 14th, 21st and 28th day of storage. Beverages containing L. paracasei Lpc-37TM or L. rhamnosus HN001TM were characterized by a sig- nificantly higher average number of viable cells (7.02 or 7.05 log cfu/g, respectively) than products with lactis HN019TM or L. acidophilus NCFM® (6.43 or 6.37 log cfu/g, respectively). The use of L. paracasei Lpc-37 and L. rhamnosus HN001 strains in orange and apple drinks allows the recommended count for probiotic products, 106 cfu/g for 28 days of storage, to be exceeded. Survival of the B. lactis HN019 strain fulfills the above requirements only in the orange drink. The L. acidophilus NCFM® strain was found to be the least suitable for the production of beverages, as it did not reach 6 log cfu/g in any products after 28 days of stor- age. The highest average number of bacteria was found in the orange beverages (7.14 log cfu/g). In terms of bacteria viability, blackcurrant juice was the least suitable for the production of whey probiotic drinks, due to its high acidity. The results of the present study indicate that careful selection of the fruit juice component, especially in terms of its acidity, is key to designing successful probiotic fruit-whey beverages. Other factors which should be taken into account to ensure a sufficient number of live probiotic cells, i.e. their therapeutic level in fruit-whey drinks, are the choice of probiotic strain and determination of the maximal shelf life.

Quantitative Analysis of Land Loss in Coastal Louisiana Using Remote Sensing

NASA Astrophysics Data System (ADS)

Wales, P. M.; Kuszmaul, J.; Roberts, C.

2005-12-01

For the past thirty-five years the land loss along the Louisiana Coast has been recognized as a growing problem. One of the clearest indicators of this land loss is that in 2000 smooth cord grass (spartina alterniflora) was turning brown well before its normal hibernation period. Over 100,000 acres of marsh were affected by the 2000 browning. In 2001 data were collected using low altitude helicopter based transects of the coast, with 7,400 data points being collected by researchers at the USGS, National Wetlands Research Center, and Louisiana Department of Natural Resources. The surveys contained data describing the characteristics of the marsh, including latitude, longitude, marsh condition, marsh color, percent vegetated, and marsh die-back. Creating a model that combines remote sensing images, field data, and statistical analysis to develop a methodology for estimating the margin of error in measurements of coastal land loss (erosion) is the ultimate goal of the study. A model was successfully created using a series of band combinations (used as predictive variables). The most successful band combinations or predictive variables were the braud value [(Sum Visible TM Bands - Sum Infrared TM Bands)/(Sum Visible TM Bands + Sum Infrared TM Bands)], TM band 7/ TM band 2, brightness, NDVI, wetness, vegetation index, and a 7x7 autocovariate nearest neighbor floating window. The model values were used to generate the logistic regression model. A new image was created based on the logistic regression probability equation where each pixel represents the probability of finding water or non-water at that location in each image. Pixels within each image that have a high probability of representing water have a value close to 1 and pixels with a low probability of representing water have a value close to 0. A logistic regression model is proposed that uses seven independent variables. This model yields an accurate classification in 86.5% of the locations considered in the 1997 and 2001 survey locations. When the logistic regression was modeled to the satellite imagery of the entire Louisiana Coast study area a statewide loss was estimated to be 358 mi2 to 368 mi2, from 1997 to 2001, using two different methods for estimating land loss.

Double NIR laser stimulation and enhancing the thermal sensitivity of Er3+/Tm3+/Nd3+ doped multilayer core-shell nanoparticles.

PubMed

Ba, Zhaojing; Hu, Min; Zhao, Yiming; Wang, Yiqing; Wang, Jing; Zhang, Zhenxi

2018-08-31

Non-contact thermal sensors are important devices to study cellular processes and monitor temperature in vivo. Herein, a novel highly sensitive nanothermometer based on NaYF 4 :Yb,Er@ NaYF 4 @NaYF 4 :Yb,Tm@ NaYF 4 :Nd (denoted as Er@Y@Tm@Nd) was prepared by a facile solvothermal method. When excited by the near-infrared (NIR) light of 808 and 980 nm, the as-prepared Er@Y@Tm@Nd nanoparticles could emit both blue and green light, respectively, since the lanthanide cations responsible for these emissions are gathered inside this nanostructure. The green and blue light intensity ratio exhibits obvious temperature dependence in the range of the physiological temperature. Additionally, the fluorescence intensity of Er 3+ and Tm 3+ are also greatly enhanced due to the multilayer structure that implies avoiding the Er 3+ and Tm 3+ energy cross-relaxation by introduction of a NaYF 4 wall between them. The as-prepared core-shell-shell-shell structure with Er 3+ and Tm 3+ in different layers improves dozens of times of the thermal sensitivity based on the non-thermal coupling levels of the probe: the maximum values for the sensitivity are 2.95% K -1 (I Er-521 /I Tm-450 ) and 6.30% K -1 (I Tm-474 /I Er-541 ) when excited by 980 and 808 nm laser sources, respectively. These values are well above those previously reported (<0.7% K -1 ), indicating that the prepared nanostructures are temperature sensors with excellent thermal sensitivity and sensitive to NIR wavelength excitation that makes them highly preferred for thermal detection.

Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein-coupled receptors

PubMed Central

Yin, Yanting; de Waal, Parker W.; He, Yuanzheng; Zhao, Li-Hua; Yang, Dehua; Cai, Xiaoqing; Jiang, Yi; Melcher, Karsten; Wang, Ming-Wei; Xu, H. Eric

2017-01-01

The glucagon receptor (GCGR) belongs to the secretin-like (class B) family of G protein-coupled receptors (GPCRs) and is activated by the peptide hormone glucagon. The structures of an activated class B GPCR have remained unsolved, preventing a mechanistic understanding of how these receptors are activated. Using a combination of structural modeling and mutagenesis studies, we present here two modes of ligand-independent activation of GCGR. First, we identified a GCGR-specific hydrophobic lock comprising Met-338 and Phe-345 within the IC3 loop and transmembrane helix 6 (TM6) and found that this lock stabilizes the TM6 helix in the inactive conformation. Disruption of this hydrophobic lock led to constitutive G protein and arrestin signaling. Second, we discovered a polar core comprising conserved residues in TM2, TM3, TM6, and TM7, and mutations that disrupt this polar core led to constitutive GCGR activity. On the basis of these results, we propose a mechanistic model of GCGR activation in which TM6 is held in an inactive conformation by the conserved polar core and the hydrophobic lock. Mutations that disrupt these inhibitory elements allow TM6 to swing outward to adopt an active TM6 conformation similar to that of the canonical β2-adrenergic receptor complexed with G protein and to that of rhodopsin complexed with arrestin. Importantly, mutations in the corresponding polar core of several other members of class B GPCRs, including PTH1R, PAC1R, VIP1R, and CRFR1, also induce constitutive G protein signaling, suggesting that the rearrangement of the polar core is a conserved mechanism for class B GPCR activation. PMID:28356352

Rearrangement of a polar core provides a conserved mechanism for constitutive activation of class B G protein-coupled receptors.

PubMed

Yin, Yanting; de Waal, Parker W; He, Yuanzheng; Zhao, Li-Hua; Yang, Dehua; Cai, Xiaoqing; Jiang, Yi; Melcher, Karsten; Wang, Ming-Wei; Xu, H Eric

2017-06-16

The glucagon receptor (GCGR) belongs to the secretin-like (class B) family of G protein-coupled receptors (GPCRs) and is activated by the peptide hormone glucagon. The structures of an activated class B GPCR have remained unsolved, preventing a mechanistic understanding of how these receptors are activated. Using a combination of structural modeling and mutagenesis studies, we present here two modes of ligand-independent activation of GCGR. First, we identified a GCGR-specific hydrophobic lock comprising Met-338 and Phe-345 within the IC3 loop and transmembrane helix 6 (TM6) and found that this lock stabilizes the TM6 helix in the inactive conformation. Disruption of this hydrophobic lock led to constitutive G protein and arrestin signaling. Second, we discovered a polar core comprising conserved residues in TM2, TM3, TM6, and TM7, and mutations that disrupt this polar core led to constitutive GCGR activity. On the basis of these results, we propose a mechanistic model of GCGR activation in which TM6 is held in an inactive conformation by the conserved polar core and the hydrophobic lock. Mutations that disrupt these inhibitory elements allow TM6 to swing outward to adopt an active TM6 conformation similar to that of the canonical β 2 -adrenergic receptor complexed with G protein and to that of rhodopsin complexed with arrestin. Importantly, mutations in the corresponding polar core of several other members of class B GPCRs, including PTH1R, PAC1R, VIP1R, and CRFR1, also induce constitutive G protein signaling, suggesting that the rearrangement of the polar core is a conserved mechanism for class B GPCR activation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Predictions Suggesting a Participation of β-Sheet Configuration in the M2 Domain of the P2X7 Receptor: A Novel Conformation?

PubMed Central

Teixeira, Pedro Celso Nogueira; de Souza, Cristina Alves Magalhães; de Freitas, Mônica Santos; Foguel, Débora; Caffarena, Ernesto Raul; Alves, Luiz Anastacio

2009-01-01

Scanning experiments have shown that the putative TM2 domain of the P2X7 receptor (P2X7R) lines the ionic pore. However, none has identified an α-helix structure, the paradigmatic secondary structure of ion channels in mammalian cells. In addition, some researchers have suggested a β-sheet conformation in the TM2 domain of P2X2. These data led us to investigate a new architecture within the P2X receptor family. P2X7R is considered an intriguing receptor because its activation induces nonselective large pore formation, in contrast to the majority of other ionic channel proteins in mammals. This receptor has two states: a low-conductance channel (∼10 pS) and a large pore (>400 pS). To our knowledge, one fundamental question remains unanswered: Are the P2X7R channel and the pore itself the same entity or are they different structures? There are no structural data to help solve this question. Thus, we investigated the hydrophobic M2 domain with the aim of predicting the fitted position and the secondary structure of the TM2 segment from human P2X7R (hP2X7R). We provide evidence for a β-sheet conformation, using bioinformatics algorithms and molecular-dynamics simulation in conjunction with circular dichroism in different environments and Fourier transform infrared spectroscopy. In summary, our study suggests the possibility that a segment composed of residues from part of the M2 domain and part of the putative TM2 segment of P2X7R is partially folded in a β-sheet conformation, and may play an important role in channel/pore formation associated with P2X7R activation. It is important to note that most nonselective large pores have a transmembrane β-sheet conformation. Thus, this study may lead to a paradigmatic change in the P2X7R field and/or raise new questions about this issue. PMID:19186133

Candidate-gene association study of mothers with pre-eclampsia, and their infants, analyzing 775 SNPs in 190 genes.

PubMed

Goddard, Katrina A B; Tromp, Gerard; Romero, Roberto; Olson, Jane M; Lu, Qing; Xu, Zhiying; Parimi, Neeta; Nien, Jyh Kae; Gomez, Ricardo; Behnke, Ernesto; Solari, Margarita; Espinoza, Jimmy; Santolaya, Joaquin; Chaiworapongsa, Tinnakorn; Lenk, Guy M; Volkenant, Kimberly; Anant, Madan Kumar; Salisbury, Benjamin A; Carr, Janet; Lee, Min Soeb; Vovis, Gerald F; Kuivaniemi, Helena

2007-01-01

Pre-eclampsia (PE) affects 5-7% of pregnancies in the US, and is a leading cause of maternal death and perinatal morbidity and mortality worldwide. To identify genes with a role in PE, we conducted a large-scale association study evaluating 775 SNPs in 190 candidate genes selected for a potential role in obstetrical complications. SNP discovery was performed by DNA sequencing, and genotyping was carried out in a high-throughput facility using the MassARRAY(TM) System. Women with PE (n = 394) and their offspring (n = 324) were compared with control women (n = 602) and their offspring (n = 631) from the same hospital-based population. Haplotypes were estimated for each gene using the EM algorithm, and empirical p values were obtained for a logistic regression-based score test, adjusted for significant covariates. An interaction model between maternal and offspring genotypes was also evaluated. The most significant findings for association with PE were COL1A1 (p = 0.0011) and IL1A (p = 0.0014) for the maternal genotype, and PLAUR (p = 0.0008) for the offspring genotype. Common candidate genes for PE, including MTHFR and NOS3, were not significantly associated with PE. For the interaction model, SNPs within IGF1 (p = 0.0035) and IL4R (p = 0.0036) gave the most significant results. This study is one of the most comprehensive genetic association studies of PE to date, including an evaluation of offspring genotypes that have rarely been considered in previous studies. Although we did not identify statistically significant evidence of association for any of the candidate loci evaluated here after adjusting for multiple testing using the false discovery rate, additional compelling evidence exists, including multiple SNPs with nominally significant p values in COL1A1 and the IL1A region, and previous reports of association for IL1A, to support continued interest in these genes as candidates for PE. Identification of the genetic regulators of PE may have broader implications, since women with PE are at increased risk of death from cardiovascular diseases later in life.

cDNA identification, comparison and phylogenetic aspects of lombricine kinase from two oligochaete species.

PubMed

Doumen, Chris

2010-06-01

Creatine kinase and arginine kinase are the typical representatives of an eight-member phosphagen kinase family, which play important roles in the cellular energy metabolism of animals. The phylum Annelida underwent a series of evolutionary processes that resulted in rapid divergence and radiation of these enzymes, producing the greatest diversity of the phosphagen kinases within this phylum. Lombricine kinase (EC 2.7.3.5) is one of such enzymes and sequence information is rather limited compared to other phosphagen kinases. This study presents data on the cDNA sequences of lombricine kinase from two oligochaete species, the California blackworm (Lumbriculus variegatus) and the sludge worm (Tubifex tubifex). The deduced amino acid sequences are analyzed and compared with other selected phosphagen kinases, including two additional lombricine kinase sequences extracted from DNA databases and provide further insights in the evolution and position of these enzymes within the phosphagen kinase family. The data confirms the presence of a deleted region within the flexible loop (the GS region) of all six examined lombricine kinases. A phylogenetic analysis of these six lombricine kinases clearly positions the enzymes together in a small subcluster within the larger creatine kinase (EC 2.7.3.2) clade. 2010. Published by Elsevier Inc.

Landsat sensor performance: history and current status

USGS Publications Warehouse

Markham, B.L.; Storey, James C.; Williams, Darrel L.; Irons, J.R.

2004-01-01

The current Thematic Mapper (TM) class of Landsat sensors began with Landsat-4, which was launched in 1982. This series continued with the nearly identical sensor on Landsat-5, launched in 1984. The final sensor in the series was the Landsat-7 Enhanced Thematic Mapper Plus (ETM+), which was carried into orbit in 1999. Varying degrees of effort have been devoted to the characterization of these instruments and data over the past 22 years. Extensive short-lived efforts early in the history, very limited efforts in the middle years, and now a systematic program for continuing characterization of all three systems are apparent. Currently, both the Landsat-5 TM and the Landsat-7 ETM+ are operational and providing data. Despite 20+ years of operation, the TM on Landsat-5 is fully functional, although downlinks for the data are limited. Landsat-7 ETM+ experienced a failure of its Scan Line Corrector mechanism in May 2003. Although there are gaps in the data coverage, the data remain of equivalent quality to prefailure data. Data products have been developed to fill these gaps using other ETM+ scenes.

Revised landsat-5 thematic mapper radiometric calibration

USGS Publications Warehouse

Chander, G.; Markham, B.L.; Barsi, J.A.

2007-01-01

Effective April 2, 2007, the radiometric calibration of Landsat-5 (L5) Thematic Mapper (TM) data that are processed and distributed by the U.S. Geological Survey (USGS) Center for Earth Resources Observation and Science (EROS) will be updated. The lifetime gain model that was implemented on May 5, 2003, for the reflective bands (1-5, 7) will be replaced by a new lifetime radiometric-calibration curve that is derived from the instrument's response to pseudoinvariant desert sites and from cross calibration with the Landsat-7 (L7) Enhanced TM Plus (ETM+). Although this calibration update applies to all archived and future L5 TM data, the principal improvements in the calibration are for the data acquired during the first eight years of the mission (1984-1991), where the changes in the instrument-gain values are as much as 15%. The radiometric scaling coefficients for bands 1 and 2 for approximately the first eight years of the mission have also been changed. Users will need to apply these new coefficients to convert the calibrated data product digital numbers to radiance. The scaling coefficients for the other bands have not changed.

AN EVALUATION OF THREE CONVENTIONAL HISTOLOGICAL TECHNIQUES FOR STAINING THE CERATA OF CRATENA PILATA

EPA Science Inventory

Fixation and staining methods for different types of tissue in the marine nudibranch Cratena pilata were evaluated. Cratena pilata, a marine snail in the Phylum Mollusca, has the ability to take stinging cells, called nematocysts, from ingested animals belonging to another phylum...

The type IX secretion system is required for virulence of the fish pathogen Flavobacterium columnare

USDA-ARS?s Scientific Manuscript database

Flavobacterium columnare, a member of the phylum Bacteroidetes, causes columnaris disease in wild and aquaculture-reared freshwater fish. The mechanisms responsible for columnaris disease are not known. Many members of the phylum Bacteroidetes use type IX secretion systems (T9SSs) to secrete enzymes...

Genomic understanding of dinoflagellates.

PubMed

Lin, Senjie

2011-01-01

The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates. Copyright © 2011 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

Fisetin Protects PC12 Cells from Tunicamycin-Mediated Cell Death via Reactive Oxygen Species Scavenging and Modulation of Nrf2-Driven Gene Expression, SIRT1 and MAPK Signaling in PC12 Cells.

PubMed

Yen, Jui-Hung; Wu, Pei-Shan; Chen, Shu-Fen; Wu, Ming-Jiuan

2017-04-17

Fisetin (3,7,3',4'-tetrahydroxyflavone) is a dietary flavonol and exhibits antioxidant, anti-inflammatory, and neuroprotective activities. However, high concentration of fisetin is reported to produce reactive oxygen species (ROS), induce endoplasmic reticulum (ER) stress and cause cytotoxicity in cancer cells. The aim of this study is to investigate the cytoprotective effects of low concentration of fisetin against tunicamycin (Tm)-mediated cytotoxicity in neuronal-like catecholaminergic PC12 cells. Cell viability was assayed by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and apoptotic and autophagic markers were analyzed by Western blot. Gene expression of unfolded protein response (UPR) and Phase II enzymes was further investigated using RT-Q-PCR or Western blotting. Intracellular ROS level was measured using 2',7'-dichlorodihydrofluorescein diacetate (H₂DCFDA) by a fluorometer. The effects of fisetin on mitogen activated protein kinases (MAPKs) and SIRT1 (Sirtuin 1) signaling pathways were examined using Western blotting and specific inhibitors. Fisetin (<20 µM) restored cell viability and repressed apoptosis, autophagy and ROS production in Tm-treated cells. Fisetin attenuated Tm-mediated expression of ER stress genes, such as glucose-regulated proteins 78 (GRP78), C/EBP homologous protein (CHOP also known as GADD153) and Tribbles homolog 3 (TRB3), but induced the expression of nuclear E2 related factor (Nrf)2-targeted heme oxygenase (HO)-1, glutamate cysteine ligase (GCL) and cystine/glutamate transporter (xCT/SLC7A11), in both the presence and absence of Tm. Moreover, fisetin enhanced phosphorylation of ERK (extracellular signal-regulated kinase), JNK (c-JUN NH₂-terminal protein kinase), and p38 MAPK. Addition of JNK and p38 MAPK inhibitor significantly antagonized its cytoprotective activity and modulatory effects on UPR. Fisetin also restored Tm-inhibited SIRT1 expression and addition of sirtinol (SIRT1 activation inhibitor) significantly blocked fisetin-mediated cytoprotection. In conclusion, this result shows that fisetin activates Nrf2, MAPK and SIRT1, which may elicit adaptive cellular stress response pathways so as to protect cells from Tm-induced cytotoxicity.

Atomic Resolution Structural and Chemical Imaging Revealing the Sequential Migration of Ni, Co, and Mn upon the Battery Cycling of Layered Cathode

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

Yan, Pengfei; Zheng, Jianming; Zhang, Ji-Guang

Layered lithium transition metal oxides (LTMO) are promising candidate cathode materials for next generation high energy density lithium ion battery. The challenge for using this category of cathode is the capacity and voltage fading, which is believed to be associated with the layered structure disordering, a process that is initiated from the surface or solid-electrolyte interface and facilitated by transition metal (TM) reduction and oxygen vacancy formation. However, the atomic level dynamic mechanism of such a layered structure disordering is still not fully clear. In this work, utilizing atomic resolution electron energy loss spectroscopy (EELS), we map, for the firstmore » time at atomic scale, the spatial evolution of Ni, Co and Mn in a cycled LiNi1/3M1/3Co1/3O2 layered cathode. In combination with atomic level structural imaging, we discovered the direct correlation of TM ions migration behavior with lattice disordering, featuring the residing of TM ions in the tetrahedral site and a sequential migration of Ni, Co, and Mn upon the increased lattice disordering of the layered structure. This work highlights that Ni ions, though acting as the dominant redox species in many LTMO, are labile to migrate to cause lattice disordering upon battery cycling; while the Mn ions are more stable as compared with Ni and Co and can act as pillar to stabilize layered structure. Direct visualization of the behavior of TM ions during the battery cycling provides insight for designing of cathode with structural stability and correspondingly a superior performance.« less

[Isolation and characterization of Thermopirellula anaerolimosa gen. nov., sp. nov., an obligate anaerobic hydrogen-producing bacterium of the phylum Planctomycetes].

PubMed

Liu, Dongying; Liu, Yi; Men, Xuehui; Guo, Qunqun; Guo, Rongbo; Qiu, Yanling

2012-08-04

To cultivate various yet-to-be cultured heterotrophs from anaerobic granule sludge, we used a selective culture medium with low concentrations of substrates supplemented a variety of antibiotics. An obligate anaerobic, thermophilic, hydrogen-producing bacterium, strain VM20-7(T), was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating high-strength organic wastewater from isomerized sugar production processes. Cells of strain VM20-7(T) are non-motile, spherical, pear or teardrop shaped, occurring singly(o)r as aggregates (0.7 - 2.0 microm x 0.7 - 2.0 microm). Spore formation was not observed. Growth temperature ranges from 35 - 50 degrees C (optimum 45 degrees C), pH ranges from 6.0 - 8.3 (optimum 7.0 - 7.5) , NaCl tolerant concentration ranges from 0% - 0.5% (w/v, optimum 0% ). Nitrate, sulfate, thiosulfate, sulfite, elemental sulfur and Fe (III)-NTA were not used as terminal electron acceptors. Strain VM20-7(T) utilizes a wide range of carbohydrates, including glucose, maltose, ribose, xylose, sucrose, galactose, mannose, raffinose, pectin, yeast extract and xylan. Acetate and H2 are the main end products of glucose fermentation. The G + C content of the genomic DNA was 60.9 mol%. 16S rRNA gene sequence analysis revealed that it is related to the Pirellula-Rhodopirellula-Blastopirellula (PRB) clade within the order Planctomycetales (82.7 - 84.3% similarity with 16S rRNA genes of other known related species). The first obligate anaerobic bacterium within the phylum Planctomycetes was isolated with low concentration of carbohydrates and antibiotics. On the basis of the physiological and phylogenetic data, the name Thermopirellula anaerolimosa gen. nov. , sp. nov. is proposed for strain VM20-7(T) (= CGMCC 1.5169(T) = JCM 17478(T) = DSM 24165(T)).

Complex archaea that bridge the gap between prokaryotes and eukaryotes

PubMed Central

Martijn, Joran; Lind, Anders E.; van Eijk, Roel; Schleper, Christa; Guy, Lionel; Ettema, Thijs J. G.

2015-01-01

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of ‘Lokiarchaeota’, a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic ‘starter-kit’ to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes. PMID:25945739

[Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia].

PubMed

Kalyzhnaya, O V; Itskovich, V B

2014-07-01

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria,. Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It seems likely that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.

Synergic in vitro combinations of artemisinin, pyrimethamine and methylene blue against Neospora caninum.

PubMed

Pereira, Luiz Miguel; de Luca, Gabriela; Abichabki, Nathália de Lima Martins; Bronzon da Costa, Cássia Mariana; Yatsuda, Ana Patrícia

2018-01-15

Neospora caninum is a member of Apicomplexa phylum, the causative agent of neosporosis. The neosporosis combat is not well established and several strategies related to vaccine, chemotherapy and immune modulation are under development. In this work, we evaluated the effects of artemisinin (Art), methylene blue (MB) and pyrimethamine (Pyr) alone or associated, on N. caninum proliferation and elimination using LacZ tagged tachyzoites. The reactive oxygen species (ROS) production after incubation with Art were also performed. Our results indicate that combinations of classical antimalarial drugs improve the parasite control, allowing the use of three drugs in a single dose. Additionally, artemisinin demonstrated distinct ROS production patterns in intra and extracellular N. caninum forms. The drug repurposing appears as a suitable approach, allowing a fast and safe method to evaluate old drugs but novel candidates against neosporosis. Copyright © 2017 Elsevier B.V. All rights reserved.

A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa.

PubMed

Kroer, Paul; Kjeldsen, Kasper U; Nyengaard, Jens R; Schramm, Andreas; Funch, Peter

2016-01-01

Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name "Candidatus Tenuibacter priapulorum". Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.

A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa

PubMed Central

Kroer, Paul; Kjeldsen, Kasper U.; Nyengaard, Jens R.; Schramm, Andreas; Funch, Peter

2016-01-01

Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name “Candidatus Tenuibacter priapulorum”. Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa. PMID:27199899

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples

PubMed Central

Yan, Yong-Wei; Zou, Bin; Zhu, Ting; Hozzein, Wael N.

2017-01-01

RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5’ adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10–100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples. PMID:29016661

Atomic layer deposition of highly-doped Er:Al2O3 and Tm:Al2O3 for silicon-based waveguide amplifiers (Conference Presentation)

NASA Astrophysics Data System (ADS)

Roenn, John; Karvonen, Lasse; Pyymäki-Perros, Alexander; Peyghambarian, Nasser; Lipsanen, Harri; Säynätjoki, Antti; Sun, Zhipei

2016-05-01

Recently, rare-earth doped waveguide amplifiers (REDWAs) have drawn significant attention as a promising solution to on-chip amplification of light in silicon photonics and integrated optics by virtue of their high excited state lifetime (up to 10 ms) and broad emission spectrum (up to 200 nm) at infrared wavelengths. In the family of rare-earths, at least erbium, holmium, thulium, neodymium and ytterbium have been demonstrated to be good candidates for amplifier operation at moderate concentrations (< 0.1 %). However, efficient amplifier operation in REDWAs is a very challenging task because high concentration of ions (<0.1%) is required in order to produce reasonable amplification over short device length. Inevitably, high concentration of ions leads to energy-transfer between neighboring ions, which results as decreased gain and increased noise in the amplifier system. It has been shown that these energy-transfer mechanisms in highly-doped gain media are inversely proportional to the sixth power of the distance between the ions. Therefore, novel fabrication techniques with the ability to control the distribution of the rare-earth ions within the gain medium are urgently needed in order to fabricate REDWAs with high efficiency and low noise. Here, we show that atomic layer deposition (ALD) is an excellent technique to fabricate highly-doped (<1%) RE:Al2O3 gain materials by using its nanoscale engineering ability to delicately control the incorporation of RE ions during the deposition. In our experiment, we fabricated Er:Al2O3 and Tm:Al2O3 thin films with ALD by varying the concentration of RE ions from 1% to 7%. By measuring the photoluminescence response of the fabricated samples, we demonstrate that it is possible to incorporate up to 5% of either Er- or Tm-ions in Al2O3 host before severe quenching occurs. We believe that this technique can be extended to other RE ions as well. Therefore, our results show the exceptionality of ALD as a deposition technique for REDWA technology.

Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants

NASA Astrophysics Data System (ADS)

Renard, Pascal; Canet, Isabelle; Sancelme, Martine; Wirgot, Nolwenn; Deguillaume, Laurent; Delort, Anne-Marie

2016-09-01

A total of 480 microorganisms collected from 39 clouds sampled at the Puy de Dôme station (alt. 1465 m; 45°46'19'' N, 2°57'52'' E; Massif Central, France) were isolated and identified. This unique collection was screened for biosurfactant (surfactants of microbial origin) production by measuring the surface tension (σ) of the crude extracts, comprising the supernatants of the pure cultures, using the pendant drop technique. The results showed that 41 % of the tested strains were active producers (σ < 55 mN m-1), with 7 % being extremely active (σ < 30 mN m-1). The most efficient biosurfactant producers (σ < 45 mN m-1) belong to a few bacterial genera (Pseudomonas and Xanthomonas) from the Υ-Proteobacteria class (78 %) and a yeast genus (Udeniomyces) from the Basidiomycota phylum (11 %). Some Bacillus strains from the Firmicutes phylum were also active but represented a small fraction of the collected population. Strains from the Actinobacteria phylum in the collection examined in the present study showed moderate biosurfactant production (45<σ < 55 mN m-1). Pseudomonas (Υ-Proteobacteria), the most frequently detected genus in clouds, with some species issued from the phyllosphere, was the dominant group for the production of biosurfactants. We observed some correlations between the chemical composition of cloud water and the presence of biosurfactant-producing microorganisms, suggesting the "biogeography" of this production. Moreover, the potential impact of the production of biosurfactants by cloud microorganisms on atmospheric processes is discussed.

2  μm laser oscillation of Ho3+:Tm3+-codoped silica microspheres.

PubMed

Peng, Longxiang; Huang, Yantang; Duan, Yafan; Zhuang, Shijian; Liao, Tingdi; Xu, Canhua

2017-09-10

2 μm laser oscillation with a low threshold has been achieved in Ho 3+ :Tm 3+ -codoped silica microspheres (HTCSMs). Ho 3+ :Tm 3+ -codoped solgel functionalization film is applied to the surface of a silica microsphere, and an optical tapered fiber is adopted to couple an 808 nm continuous-wave laser to serve as the pump light source. Multimode and single-mode laser oscillations around 2 μm within the eye-safe wave band are observed due to the I 7 5→I 8 5 transitions of Ho 3+ ions sensitized by Tm 3+ . The morphology characteristics of microspheres determine the multimode laser oscillation spectrum. The free spectral range is in good accordance with the calculated value based on Mie scattering theory. The HTCSM laser oscillation shows characteristics of good capability, simple process, high flexibility, and low cost.

Laparoscopic supracervical hysterectomy with transcervical morcellation: our experience.

PubMed

Graziano, Angela; Lo Monte, Giuseppe; Hanni, Herbert; Brugger, Johann Georg; Engl, Bruno; Marci, Roberto

2015-02-01

To present our experience with laparoscopic supracervical hysterectomy with transcervical morcellation (LSH-TM). A retrospective observational study (Canadian Task Force Classification III). Gynecologic Department at Brunico Hospital, Brunico, Italy. Three hundred sixty-five patients affected by gynecologic benign diseases who underwent LSH-TM. A minimally invasive surgical technique for supracervical hysterectomy that involves extraction of the morcellated uterus through the cervical canal. We performed LSH-TM successfully in 365 patients; the mean (standard deviation) operating time was 72.24 (23.21) minutes. We registered no intraoperative complications. The main postoperative complications resulted in 2 cases of second-look laparoscopy because of internal bleeding, 5 cases of asymptomatic hematoma around the cervical stump, and 7 cases of pelvic pain. Our experience shows that LSH-TM is a safe and easy to perform technique and that it ensures minimal blood loss. Copyright © 2015 AAGL. Published by Elsevier Inc. All rights reserved.

Development of a data acquisition system using a RISC/UNIX TM workstation

NASA Astrophysics Data System (ADS)

Takeuchi, Y.; Tanimori, T.; Yasu, Y.

1993-05-01

We have developed a compact data acquisition system on RISC/UNIX workstations. A SUN TM SPARCstation TM IPC was used, in which an extension bus "SBus TM" was linked to a VMEbus. The transfer rate achieved was better than 7 Mbyte/s between the VMEbus and the SUN. A device driver for CAMAC was developed in order to realize an interruptive feature in UNIX. In addition, list processing has been incorporated in order to keep the high priority of the data handling process in UNIX. The successful developments of both device driver and list processing have made it possible to realize the good real-time feature on the RISC/UNIX system. Based on this architecture, a portable and versatile data taking system has been developed, which consists of a graphical user interface, I/O handler, user analysis process, process manager and a CAMAC device driver.

Binding modes of dihydroquinoxalinones in a homology model of bradykinin receptor 1.

PubMed

Ha, Sookhee N; Hey, Pat J; Ransom, Rick W; Harrell, C Meacham; Murphy, Kathryn L; Chang, Ray; Chen, Tsing-Bau; Su, Dai-Shi; Markowitz, M Kristine; Bock, Mark G; Freidinger, Roger M; Hess, Fred J

2005-05-27

We report the first homology model of human bradykinin receptor B1 generated from the crystal structure of bovine rhodopsin as a template. Using an automated docking procedure, two B1 receptor antagonists of the dihydroquinoxalinone structural class were docked into the receptor model. Site-directed mutagenesis data of the amino acid residues in TM1, TM3, TM6, and TM7 were incorporated to place the compounds in the binding site of the homology model of the human B1 bradykinin receptor. The best pose in agreement with the mutation data was selected for detailed study of the receptor-antagonist interaction. To test the model, the calculated antagonist-receptor binding energy was correlated with the experimentally measured binding affinity (K(i)) for nine dihydroquinoxalinone analogs. The model was used to gain insight into the molecular mechanism for receptor function and to optimize the dihydroquinoxalinone analogs.

Another Strategy, Detouring Potential Decay by Fast Completion of Cation Mixing

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

Liu, Shuai; Feng, Xin; Wang, Xuelong

The Li-rich layer-structured oxides are regarded one of the most promising candidates of cathode materials for high energy-density Li-ion batteries. However, the uninterrupted migration of the transition metal (TM) ions during cycling and the resultant continuous fading of their discharge potentials bring challenges to the battery design and impede their commercial applications. Various efforts have been taken to suppress the migration of the TM ions such as surface modification and elemental substitution, but no success has been achieved to date. Another strategy hereby is proposed to address these issues, in which the TM migration is promoted and the layered materialmore » is transformed to a rocksalt in the first few charge/discharge cycles by specially designing a novel Li-rich layer-structured Li 1.2Mo 0.6Fe 0.2O 2 on the basis of density functional theory calculations. With such, the continuous falling of the discharge potential is detoured due to enhanced completion of the cation mixing. In-depth studies such as aberration-corrected scanning transmission electron microscopy confirm the drastic structural change at the atomic scale, and in situ X-ray absorption spectroscopy and Mössbauer spectroscopy clarify its charge compensation mechanism. In conclusion, this new strategy provides revelation for the development of the Li-rich layered oxides with mitigated potential decay and a longer lifespan.« less

Another Strategy, Detouring Potential Decay by Fast Completion of Cation Mixing

DOE PAGES

Liu, Shuai; Feng, Xin; Wang, Xuelong; ...

2018-02-12

The Li-rich layer-structured oxides are regarded one of the most promising candidates of cathode materials for high energy-density Li-ion batteries. However, the uninterrupted migration of the transition metal (TM) ions during cycling and the resultant continuous fading of their discharge potentials bring challenges to the battery design and impede their commercial applications. Various efforts have been taken to suppress the migration of the TM ions such as surface modification and elemental substitution, but no success has been achieved to date. Another strategy hereby is proposed to address these issues, in which the TM migration is promoted and the layered materialmore » is transformed to a rocksalt in the first few charge/discharge cycles by specially designing a novel Li-rich layer-structured Li 1.2Mo 0.6Fe 0.2O 2 on the basis of density functional theory calculations. With such, the continuous falling of the discharge potential is detoured due to enhanced completion of the cation mixing. In-depth studies such as aberration-corrected scanning transmission electron microscopy confirm the drastic structural change at the atomic scale, and in situ X-ray absorption spectroscopy and Mössbauer spectroscopy clarify its charge compensation mechanism. In conclusion, this new strategy provides revelation for the development of the Li-rich layered oxides with mitigated potential decay and a longer lifespan.« less

In vitro effects of doxorubicin and tetrathiomolybdate on canine hemangiosarcoma cells.

PubMed

Sloan, Caroline Q; Rodriguez, Carlos O

2018-02-01

OBJECTIVE To assess the in vitro effects of doxorubicin and tetrathiomolybdate (TM) on cells from a canine hemangiosarcoma cell line. SAMPLE Cultured cells from the canine hemangiosarcoma-derived cell line DEN-HSA. PROCEDURES Cells were treated with TM (0 to 1.5μM), doxorubicin (0 to 5μM), or both with or without 24 hours of pretreatment with ascorbic acid (750μM). Degree of cellular cytotoxicity was measured with a colorimetric assay. Long-term growth inhibition was assessed with a 10-day colony-formation assay. Induction of apoptosis was quantitated by fluorometric assessment of caspase-3 and -7 activation. Formation of reactive oxygen species (ROS) was also detected fluorometrically. RESULTS Exposure of cells to the combination of TM and doxorubicin resulted in a greater decrease in proliferation and clonogenic survival rates than exposure to each drug alone. This treatment combination increased ROS formation and apoptosis to a greater extent than did doxorubicin or TM alone. Ascorbic acid inhibited both TM-induced ROS formation and apoptosis. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that the enhancement in cytotoxic effects observed with DEN-HSA cell exposure to the combination of doxorubicin and TM was achieved through an increase in ROS production. These findings provide a rationale for a clinical trial of this treatment combination in dogs with hemangiosarcoma.

Identification of genes encoding the type IX secretion system and secreted proteins in Flavobacterium columnare IA-S-4

USDA-ARS?s Scientific Manuscript database

Flavobacterium columnare, a member of the phylum Bacteroidetes, causes columnaris disease in wild and aquaculture-reared freshwater fish. The mechanisms responsible for columnaris disease are not known. Many members of the phylum Bacteroidetes use type IX secretion systems (T9SSs) to secrete enzymes...

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes.

PubMed

Oren, Aharon; da Costa, Milton S; Garrity, George M; Rainey, Fred A; Rosselló-Móra, Ramon; Schink, Bernhard; Sutcliffe, Iain; Trujillo, Martha E; Whitman, William B

2015-11-01

The International Code of Nomenclature of Prokaryotes covers the nomenclature of prokaryotes up to the rank of class. We propose here modifying the Code to include the rank of phylum so that names of phyla that fulfil the rules of the Code will obtain standing in the nomenclature.

Structures and magnetic properties of Fe and Ni monoatomic chains encapsulated by an Au nanotube

NASA Astrophysics Data System (ADS)

Han, Zhi-Dong; Li, Xiu-Yan; Yang, Zhi; Liu, Rui-Ping; Liu, Shao-Ding; Zhang, Ying

2012-11-01

Structures and magnetic properties of transition metal (TM) Fe or Ni monoatomic chains (MACs) encapsulated by a Au (5, 5) nanotube (Fe@Au and Ni@Au) are investigated using the density functional theory (DFT). The calculated results show that both Fe@Au and Ni@Au prefer to adopt ferromagnetic (FM) orders as ground states. In particular, the Fe@Au keeps the magnetic properties of free-standing Fe MAC, indicating that this system may be viewed as a new candidate in electromagnetic devices.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations

PubMed Central

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E.; Geelhoed, Jeanine S.; Strous, Marc

2017-01-01

Summary For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment. PMID:28836729

Short Toxin-like Proteins Abound in Cnidaria Genomes

PubMed Central

Tirosh, Yitshak; Linial, Itai; Askenazi, Manor; Linial, Michal

2012-01-01

Cnidaria is a rich phylum that includes thousands of marine species. In this study, we focused on Anthozoa and Hydrozoa that are represented by the Nematostella vectensis (Sea anemone) and Hydra magnipapillata genomes. We present a method for ranking the toxin-like candidates from complete proteomes of Cnidaria. Toxin-like functions were revealed using ClanTox, a statistical machine-learning predictor trained on ion channel inhibitors from venomous animals. Fundamental features that were emphasized in training ClanTox include cysteines and their spacing along the sequences. Among the 83,000 proteins derived from Cnidaria representatives, we found 170 candidates that fulfill the properties of toxin-like-proteins, the vast majority of which were previously unrecognized as toxins. An additional 394 short proteins exhibit characteristics of toxin-like proteins at a moderate degree of confidence. Remarkably, only 11% of the predicted toxin-like proteins were previously classified as toxins. Based on our prediction methodology and manual annotation, we inferred functions for over 400 of these proteins. Such functions include protease inhibitors, membrane pore formation, ion channel blockers and metal binding proteins. Many of the proteins belong to small families of paralogs. We conclude that the evolutionary expansion of toxin-like proteins in Cnidaria contributes to their fitness in the complex environment of the aquatic ecosystem. PMID:23202321

Short toxin-like proteins abound in Cnidaria genomes.

PubMed

Tirosh, Yitshak; Linial, Itai; Askenazi, Manor; Linial, Michal

2012-11-16

Cnidaria is a rich phylum that includes thousands of marine species. In this study, we focused on Anthozoa and Hydrozoa that are represented by the Nematostella vectensis (Sea anemone) and Hydra magnipapillata genomes. We present a method for ranking the toxin-like candidates from complete proteomes of Cnidaria. Toxin-like functions were revealed using ClanTox, a statistical machine-learning predictor trained on ion channel inhibitors from venomous animals. Fundamental features that were emphasized in training ClanTox include cysteines and their spacing along the sequences. Among the 83,000 proteins derived from Cnidaria representatives, we found 170 candidates that fulfill the properties of toxin-like-proteins, the vast majority of which were previously unrecognized as toxins. An additional 394 short proteins exhibit characteristics of toxin-like proteins at a moderate degree of confidence. Remarkably, only 11% of the predicted toxin-like proteins were previously classified as toxins. Based on our prediction methodology and manual annotation, we inferred functions for over 400 of these proteins. Such functions include protease inhibitors, membrane pore formation, ion channel blockers and metal binding proteins. Many of the proteins belong to small families of paralogs. We conclude that the evolutionary expansion of toxin-like proteins in Cnidaria contributes to their fitness in the complex environment of the aquatic ecosystem.

Evaluation of Existing Methods for Human Blood mRNA Isolation and Analysis for Large Studies

PubMed Central

Meyer, Anke; Paroni, Federico; Günther, Kathrin; Dharmadhikari, Gitanjali; Ahrens, Wolfgang; Kelm, Sørge; Maedler, Kathrin

2016-01-01

Aims Prior to implementing gene expression analyses from blood to a larger cohort study, an evaluation to set up a reliable and reproducible method is mandatory but challenging due to the specific characteristics of the samples as well as their collection methods. In this pilot study we optimized a combination of blood sampling and RNA isolation methods and present reproducible gene expression results from human blood samples. Methods The established PAXgeneTM blood collection method (Qiagen) was compared with the more recent TempusTM collection and storing system. RNA from blood samples collected by both systems was extracted on columns with the corresponding Norgen and PAX RNA extraction Kits. RNA quantity and quality was compared photometrically, with Ribogreen and by Real-Time PCR analyses of various reference genes (PPIA, β-ACTIN and TUBULIN) and exemplary of SIGLEC-7. Results Combining different sampling methods and extraction kits caused strong variations in gene expression. The use of PAXgeneTM and TempusTM collection systems resulted in RNA of good quality and quantity for the respective RNA isolation system. No large inter-donor variations could be detected for both systems. However, it was not possible to extract sufficient RNA of good quality with the PAXgeneTM RNA extraction system from samples collected by TempusTM collection tubes. Comparing only the Norgen RNA extraction methods, RNA from blood collected either by the TempusTM or PAXgeneTM collection system delivered sufficient amount and quality of RNA, but the TempusTM collection delivered higher RNA concentration compared to the PAXTM collection system. The established Pre-analytix PAXgeneTM RNA extraction system together with the PAXgeneTM blood collection system showed lowest CT-values, i.e. highest RNA concentration of good quality. Expression levels of all tested genes were stable and reproducible. Conclusions This study confirms that it is not possible to mix or change sampling or extraction strategies during the same study because of large variations of RNA yield and expression levels. PMID:27575051

Functional characterization of GH7 endo-1,4-β-glucanase from Aspergillus fumigatus and its potential industrial application.

PubMed

Bernardi, Aline Vianna; de Gouvêa, Paula Fagundes; Gerolamo, Luis Eduardo; Yonamine, Deborah Kimie; de Lourdes de Lima Balico, Laís; Uyemura, Sergio Akira; Dinamarco, Taisa Magnani

2018-04-30

A gene encoding an endo-1,4-β-glucanase (Afu6g01800) from A. fumigatus was cloned into the vector pET-28a(+) and expressed in the E. coli strain RosettaTM (DE3) pLysS. Sequence analysis indicated that the enzyme Af-EGL7 belonged to the GH7 family. The gene Af-egl7 encoded a protein comprising 460 amino acids, with a CBM1 domain at residues 424-460 and molecular mass of 52 kDa, as estimated by SDS-PAGE. This enzyme was optimally active at pH and temperatures ranging from 4.5 to 5.5 and from 40 to 60 °C, respectively. Mn 2+ addition significantly enhanced the Af-EGL7 cellulase activity by 233%, whereas SDS addition fully inhibited this activity. Higher activity was observed toward β-glucan than toward xyloglucan and CM-Cellulose, suggesting that the enzyme corresponds to a β-1,3-1,4-glucanase. qRT-PCR in different culture media helped to establish the time-course expression profile. Different polysaccharides induced the gene Af-egl7 in a time-dependent manner; in the particular case of the substrate sugarcane exploded bagasse (SEB), Af-egl7 was induced 2500-fold. Upon addition to a commercial cellulase cocktail, Af-EGL7 significantly improved SEB saccharification, which suggested that the enzyme Af-EGL7 had great potential to hydrolyze complex biomass. From a biotechnological point of view, A. fumigatus Af-EGL7 is a promising candidate to enhance enzyme cocktails used in biorefineries such as consolidated bioprocessing. Copyright © 2018 Elsevier Inc. All rights reserved.

Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes

DOE PAGES

Kotak, Malini; Isanapong, Jantiya; Goodwin, Lynne A.; ...

2015-03-05

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. Here, we report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. In conclusion, genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.

Water regime influences bulk soil and Rhizosphere of Cereus jamacaru bacterial communities in the Brazilian Caatinga biome.

PubMed

Nessner Kavamura, Vanessa; Taketani, Rodrigo Gouvêa; Lançoni, Milena Duarte; Andreote, Fernando Dini; Mendes, Rodrigo; Soares de Melo, Itamar

2013-01-01

We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes.

Water Regime Influences Bulk Soil and Rhizosphere of Cereus jamacaru Bacterial Communities in the Brazilian Caatinga Biome

PubMed Central

Nessner Kavamura, Vanessa; Taketani, Rodrigo Gouvêa; Lançoni, Milena Duarte; Andreote, Fernando Dini; Mendes, Rodrigo; Soares de Melo, Itamar

2013-01-01

We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes. PMID:24069212

A low carbohydrate Mediterranean diet improves cardiovascular risk factors and diabetes control among overweight patients with type 2 diabetes mellitus: a 1-year prospective randomized intervention study.

PubMed

Elhayany, A; Lustman, A; Abel, R; Attal-Singer, J; Vinker, S

2010-03-01

The appropriate dietary intervention for overweight persons with type 2 diabetes mellitus (DM2) is unclear. Trials comparing the effectiveness of diets are frequently limited by short follow-up times and high dropout rates. The effects of a low carbohydrate Mediterranean (LCM), a traditional Mediterranean (TM), and the 2003 American Diabetic Association (ADA) diet were compared, on health parameters during a 12-month period. In this 12-month trial, 259 overweight diabetic patients (mean age 55 years, mean body mass index 31.4 kg/m(2)) were randomly assigned to one of the three diets. The primary end-points were reduction of fasting plasma glucose, HbA1c and triglyceride (TG) levels. 194 patients out of 259 (74.9%) completed follow-up. After 12 months, the mean weight loss for all patients was 8.3 kg: 7.7 kg for ADA, 7.4 kg for TM and 10.1 kg for LCM diets. The reduction in HbA1c was significantly greater in the LCM diet than in the ADA diet (-2.0 and -1.6%, respectively, p < 0.022). HDL cholesterol increased (0.1 mmol/l +/- 0.02) only on the LCM (p < 0.002). The reduction in serum TG was greater in the LCM (-1.3 mmol/l) and TM (-1.5 mmol/l) than in the ADA (-0.7 mmol/l), p = 0.001. An intensive 12-month dietary intervention in a community-based setting was effective in improving most modifiable cardiovascular risk factors in all the dietary groups. Only the LCM improved HDL levels and was superior to both the ADA and TM in improving glycaemic control.

Effect of supplementing different concentrations of organic trace minerals on performance, antioxidant activity, and bone mineralization in Vanaraja chickens developed for free range farming.

PubMed

Rao, Savaram Venkata Rama; Prakash, Bhukya; Kumari, Kanya; Raju, Mantena Venkata Laxmi Narasimha; Panda, Arun Kumar

2013-08-01

An experiment was conducted to determine the performance, antioxidation activity, and bone mineral content in Vanaraja chickens fed diet supplemented with organic trace minerals (oTM) at reduced levels. A total of 360 day-old chicks were selected and distributed randomly into 60 battery brooder pens. A maize-soybean meal-based control diet was supplemented with inorganic trace minerals (iTM), i.e., Mn, Zn, Fe, and Cu at 50, 45, 40, and 7.5 mg/kg, respectively, and varying concentration of oTM, i.e., Zn, Mn, Cu, Fe, I, Se, and Cr at 45, 50, 7.5, 40, 2, 0.30, and 0.25 mg/kg (diet II); 33.75, 37.50, 5.63, 30.0, 1.50, 0.23, and 0.19 mg/kg (diet III); 22.5, 25.0, 3.75, 20.0, 1.0, 0.15, and 0.13 mg/kg (diet IV); 18.0, 20.0, 3.0, 16.0, 0.80, 0.12, and 0.10 mg/kg (diet V); and 13.5, 15.0, 2.25, 12.0, 0.60, 0.09, and 0.08 mg/kg (diet VI), respectively. Each diet was allotted randomly to ten replicates and fed ad libitum from 1 to 42 days of age. The body weight at 14, 28, and 42 days was not affected by reducing the supplementation of oTM concentration in the diets. Similarly, feed intake at 14 days of age was not affected but reduced significantly (P < 0.05) in the group fed diet IV (50% oTM) compared to that in the other groups. The higher feed conversion ratio and increased concentration of Ca, P, and trace minerals in tibia were evident in the group fed oTM-supplemented diets compared to the diet containing iTM. Activities of glutathione peroxidase and ferric reducing ability in plasma did not differ in the groups fed on lower concentration of oTM compared to those fed on diet I (control diet). Therefore, it is concluded that the dietary supplementation of trace minerals can be reduced greatly when supplemented as organic form without affecting growth and antioxidant status in Vanaraja chickens.

Natural Materials and Systems

DTIC Science & Technology

2013-03-07

distribution is unlimited 7 Program Trends – BRI is biggest impact • Chromophores/Bioluminescence – Bio-X STT phase 1 focus. One of its discoveries are...C) Tm ( ferritin ) Tm (nAl) Bio-thermite complex nAl only nAl FeO(OH) TGA/DSC profile (~40-44 cages/nAl...stabilize reactive components, interact with nAl, and quickly deliver components to the surface. • Ferritin used in a single or multi-layer

Accuracy of the Estimated Core Temperature (ECTemp) Algorithm in Estimating Circadian Rhythm Indicators

DTIC Science & Technology

2017-04-12

measurement of CT outside of stringent laboratory environments. This study evaluated ECTempTM, a heart rate-based extended Kalman Filter CT...based CT-estimation algorithms [7, 13, 14]. One notable example is ECTempTM, which utilizes an extended Kalman Filter to estimate CT from...3. The extended Kalman filter mapping function variance coefficient (Ct) was computed using the following equation: = −9.1428 ×

Surficial geology of the Safsaf region, south-central Egypt, derived from remote-sensing and field data

USGS Publications Warehouse

Davis, P.A.; Breed, C.S.; McCauley, J.F.; Schaber, G.G.

1993-01-01

We used a decorrelation-stretched image of Landsat Thematic Mapper (TM) Bands 1, 4, and 7 and field data to map and describe the main surficial units in the hyperarid Safsaf region in south-central Egypt. We show that the near-infrared bands on Landsat TM, which are sensitive to very subtle changes in mineralogy common to arid regions, significantly improve the geologist's capability to discriminate geologic units in desert regions. These data also provide the spatial and spectral information necessary to determine the migration patterns and provenance of eolian materials. The Safsaf area was the focus of our post flight field studies using Shuttle Imaging Radar (SIR) data following the discovery of buried paleochannels in North Africa. Most of the channels discernible on SIR images are not expressed in TM data, but traces of a few channels are present in both the SIR and the TM data within the Wadi Safsaf area. Here we present a detailed digital examination of the SIR and the TM-band reflectance and reflectance-ratio data at three locations of the more obvious surface expressions of the buried channels. Our results indicate that the TM expressions of the channels are not purely topographic but are more compositional in nature. Two possibilities may account for the TM expressions of the buried channels: 1) concentrations of windblown, iron-rich materials that accumulated along subtle curvilinear topograpohic traps, or 2) curvilinear exposures of an iron-rich underlying unit of the flat sand sheet. ?? 1993.

Eco-design pilot project in China - Monsoon offer 2 upgrade

NASA Astrophysics Data System (ADS)

Thai, Roselyne; Liu, Guoguo

2017-11-01

During COP21, Schneider Electric has committed that 100% of our new products would be eco-designed to tackle climate change. Launched in 2015, this initiative ecoDesign WayTM was tested on some pilot projects. This project covers the first ecoDesign WayTM pilot in China on an overvoltage or under voltage protective device used in both residential and industrial sectors, called Monsoon. Under the name ecoDesign WayTM, a method and a process have been deployed. The 3 main ecoDesign WayTM phases are: phase 1 - Marketing & Technique handshake, Phase 2 - ecoDesign WayTM follow-up and Phase 3 - Marketing communication. During the project, EIME from Bureau Veritas CODDE and ecoDesign WayTM scorecard from EVEA consulting are two core tools for eco-design implementation. They are respectively used for life cycle assessment and eco-design performance comparison. Thanks to the approach, compared to previous range, pollution emissions and resource depletion along the whole life cycle of product have decreased (reduction of 55% for energy depletion and 85% for water depletion). Global warming potential has dramatically decreased by 98.4% and air pollution by 33%. Meanwhile, the recycling rate has been improved by 18%, and recycled PA is used. The ecoDesign WayTM scorecard is stored as referent document for any customer request. Moreover, customers can access RoHS certificate, REACh declaration, PEP and EoLI in Check a product, an online environmental data repository, available 24/7.

Expression of caveolin in trabecular meshwork cells and its possible implication in pathogenesis of primary open angle glaucoma

PubMed Central

Surgucheva, Irina

2011-01-01

Purpose Primary open-angle glaucoma (POAG), which is the most common form of glaucoma, has been associated with a heterogeneous genetic component. A genome-wide association study has identified a common sequence variant at 7q31 (rs4236601 [A]) near the caveolin genes in patients with POAG. Caveolins are a family of integral membrane proteins which participate in many cellular processes, including vesicular transport, cholesterol homeostasis, signal transduction, cell adhesion and migration. The goal of this study was to investigate the expression and regulation of caveolin 1 (CAV-1) and caveolin 2 (CAV-2) in normal and glaucoma trabecular meshwork (TM) cells. Methods CAV-1 and CAV-2 protein expression was quantified by immunoblot analysis using lysates isolated from primary and immortalized TM cells or TM tissue dissected from normal and POAG eyes. The localization of caveolins in TM cells was assessed by immunofluorescent microscopy. CAV-1 and CAV-2 protein expression was also investigated in TM cells at various time points after subjecting the cells to known glaucomatous insults like dexamethasone (DEX) and tumor growth factor beta2 (TGF-β2) treatment. Phosphorylation of CAV-1 at tyrosine 14 in normal and glaucoma TM cell lines was evaluated using a specific monoclonal antibody (Ab). The 5′ upstream region of the CAV-1 gene was amplified and the sequence variant rs4236601 (A/G polymorphic site) and several putative transcription factor-binding sites were modified by in vitro mutagenesis. The effect of nucleotide sequence modifications in the CAV-1 upstream region on gene expression was assayed in a luciferase-based system in TM and non-TM cells. Results CAV-1 and CAV-2 are expressed in TM cells, with localization to the cytoplasm and perinuclear region. DEX increased CAV-1 expression in immortalized glaucoma TM cells by 2.8±0.1 (n=3) fold at 24 h and 2.5±0.1 (n=3) fold at 48 h, compared to 1.3±0.06 (n=3) fold at 24 and 48 h in immortalized normal TM cells. Phosphorylation of CAV-1 at Tyr14 was reduced by 3.2±0.15 (n=3) fold in glaucomatous TM cells when compared to normal TM cells. In POAG and normal TM tissue, CAV-1 expression was found to be uniform. CAV-2, on the other hand, was variable in independent normal and glaucoma TM tissue. Substitution of a G for an A at base pair −2,388 upstream of the start codon of CAV-1, corresponding to the minor allele rs4236601 [A], increased transcriptional activity in TM and non-TM cells when compared to the native sequence. Deletion analysis of putative transcription factor binding sites in the CAV-1 promoter region caused cell-specific effects on gene expression. Conclusions CAV-1 and CAV-2 are expressed in normal and glaucoma tissue and TM cell lines. Phosphorylation of Tyr14 in CAV-1 and transcriptional regulation of CAV-1 expression may have a role in glaucomatous alterations in TM cells. PMID:22128235

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

DOE PAGES

Hiras, Jennifer; Wu, Yu-Wei; Eichorst, Stephanie A.; ...

2015-09-01

Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a larger lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided amore » consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome ( > 95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.« less

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage.

PubMed

Hiras, Jennifer; Wu, Yu-Wei; Eichorst, Stephanie A; Simmons, Blake A; Singer, Steven W

2016-04-01

Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.

Comparison of outgassing models for the landsat thematic mapper sensors

USGS Publications Warehouse

Micijevic, E.; Chander, G.

2007-01-01

The Thematic Mapper (TM) is a multi-spectral electro-optical sensor featured onboard both the Landsat 4 (L4) and Landsat 5 (L5) satellites. TM sensors have seven spectral bands with center wavelengths of approximately 0.49, 0.56, 0.66, 0.83, 1.65, 11.5 and 2.21 ??m, respectively. The visible near-infrared (VNIR) bands are located on the primary focal plane (PFP), and two short-wave infrared (SWIR) bands and the thermal infrared (TIR) band are located on the cold focal plane (CFP). The CFP bands are maintained at cryogenic temperatures of about 91 K, to reduce thermal noise effects. Due to the cold temperature, an ice film accumulates on the CFP dewar window, which introduces oscillations in SWIR and an exponential decay in TIR band responses. This process is usually monitored and characterized by the detector responses to the internal calibrator (IC) lamps and the blackbody. The ice contamination on the dewar window is an effect of the sensor outgassing in a vacuum of the space environment. Outgassing models have been developed, which are based on the thin-film optical interference phenomenon. They provide the coefficients for correction for outgassing effects for the entire mission's lifetime. While the L4 TM ceased imaging in August 1993, the L5 TM continues to operate even after more than 23 years in orbit. The process of outgassing in L5 TM is still occurring, though at a much lower rate than during early years of mission. Although the L4 and L5 TM sensors are essentially identical, they exhibit slightly different responses to the outgassing effects. The work presented in the paper summarizes the results of modeling outgassing effects in each of the sensors and provides a detailed analysis of differences among the estimated modeling parameters. For both sensors, water ice was confirmed as a reasonable candidate for contaminant material, the contaminant growth rate was found to be gradually decreasing with the time since launch, and the indications exist that some film may remain after the CFP warm-up procedures, which are periodically initiated to remove accumulated contamination. The observed difference between the models could be contributed to differences in the operational history for the sensors, the content and amount of contaminant impurities, the sensor spectral filter responses, and the internal calibrator systems.

Characterisation and luminescence studies of Tm and Na doped magnesium borate phosphors.

PubMed

Ekdal, E; Garcia Guinea, J; Karabulut, Y; Canimoglu, A; Harmansah, C; Jorge, A; Karali, T; Can, N

2015-09-01

In this study, structural and luminescence properties of magnesium borate of the form MgB4O7 doped with Tm and Na were investigated by X-ray diffraction (XRD), Raman spectroscopy and cathodoluminescence (CL). The morphologies of the synthetised compounds exhibit clustered granules and road-like materials. As doping trivalent ions into a host with divalent cations requires charge compensation, this effect is discussed. The CL spectra of undoped MgB4O7 shows a broad band emission centred around 350 nm which is postulated to be produced by self-trapped excitons and some other defects. From the CL emission spectrum, main emission bands centred at 360, 455, 475 nm due to the respective transitions of (1)D2→(3)H6,(1)D2→(3)F4 and (1)G4→(3)H6 suggest the presence of Tm(3+) ion in MgB4O7 lattice site. CL mechanism was proposed to explain the observed phenomena which are valuable in possibility of the developing new luminescent materials for different applications. In addition, the experimental Raman spectrum of doped and undoped MgB4O7 were reported and discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium.

PubMed

Huang, Po-Jung Jimmy; Vazin, Mahsa; Liu, Juewen

2015-10-20

Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).

Thematic mapper studies of central Andean volcanoes

NASA Technical Reports Server (NTRS)

Francis, Peter W.

1987-01-01

A series of false color composite images covering the volcanic cordillera was written. Each image is 45 km (1536 x 1536 pixels) and was constructed using bands 7, 4, and 2 of the Thematic Mapper (TM) data. Approximately 100 images were prepared to date. A set of LANDSAT Multispectral Scanner (MSS) images was used in conjunction with the TM hardcopy to compile a computer data base of all volcanic structure in the Central Andean province. Over 500 individual structures were identified. About 75 major volcanoes were identified as active, or potentially active. A pilot study was begun combining Shuttle Imaging Radar (SIR) data with TM for a test area in north Chile and Bolivia.

A multiplexed method for kinetic measurements of apoptosis and proliferation using live-content imaging.

PubMed

Artymovich, Katherine; Appledorn, Daniel M

2015-01-01

In vitro cell proliferation and apoptosis assays are widely used to study cancer cell biology. Commonly used methodologies are however performed at a single, user-defined endpoint. We describe a kinetic multiplex assay incorporating the CellPlayer(TM) NucLight Red reagent to measure proliferation and the CellPlayer(TM) Caspase-3/7 reagent to measure apoptosis using the two-color, live-content imaging platform, IncuCyte(TM) ZOOM. High-definition phase-contrast images provide an additional qualitative validation of cell death based on morphological characteristics. The kinetic data generated using this strategy can be used to derive informed pharmacology measurements to screen potential cancer therapeutics.

Relationship Between the Melting Temperature of hcp Iron at ICB Pressure and the Light Impurity Content of Earth's Core

NASA Astrophysics Data System (ADS)

Anderson, O. L.

2001-12-01

The table below leads the reader through calculation of the core density deficit starting from the melting temperature (solidus), Tm, at the pressure, P, of the inner core boundary (ICB) (330 GPa). Tm values come from recent data of four sets of authors. Thermal pressure, Δ PTH, values were calculated in the author's laboratory. P0 = 330 - PTH is the P corresponding to the volume, V, of iron at Tm, V0 (sol.). P0 yields V0 (sol.) from an equation of state. The volume change of melting, Δ Vm, which leads to the liquidus V, V0 (liq.), was determined by the author. The liquidus density, ρ 0 (liq.), is higher than the seismic density at 330 GPa by the core density deficit. S wt.% is the amount of sulfur alone that satisfies the core ρ deficit. Δ Tf is the freezing point depression arising from impurities. %table { \\setlength{\\tabcolsep}{.05truein} \\begin{center} \\begin{tabular}{lcccc} \\multicolumn{5}{l}{ Core density deficit and freezing point depression} multicolumn{5}{l}{calculated from Tm} \\hline Tm (330)& 4800 K& 5850 K& 6700 K& 7500 K \\hline Δ PTH& 64.0& 82.0& 97.0& 112\\P0 (330 K)& 266& 248& 233& 218\\V0 (sol.)& 4.25& 4.30& 4.37& 4.43Δ Vm& .055& .055& .055& .055\\V0 (liq.)& 4.305& 4.355& 4.425& 4.485ρ (liq.)& 13.09& 12.94& 12.73& 12.48 core ρ def.& 7.1& 6& 4& 2.9 S wt.% & 7.3& 6.2& 3.8& 2.5 Δ Tf& ~ 330& ~ 300& ~ 200& ~ 150 \\hline \\multicolumn{5}{l}{Units: PTH & P0, GPa; V0 & Δ Vm, cm3mol.-1;} multicolumn{5}{l}{ρ , kg m-3x 103; core ρ def., %; Δ Tf, K.}\\ } Cosmochemists' estimates of viable amounts of S and Si in the core are most easily satisfied by the core density deficit arising from Tm = 5850 K. High Tm values result in surprisingly high values for Earth's ICB temperature, because Δ Tf is low. A large Δ PTH results in a low Δ Tf.

Landsat thematic mapper (TM) soil variability analysis over Webster County, Iowa

NASA Technical Reports Server (NTRS)

Thompson, D. R.; Henderson, K. E.; Pitts, D. E.

1984-01-01

Thematic mapper simulator (TMS) data acquired June 7, June 23, and July 31, 1982, and Landsat thematic mapper (TM) data acquired August 2, September 3, and October 21, 1982, over Webster County, Iowa, were examined for within-field soil effects on corn and soybean spectral signatures. It was found that patterns displayed on various computer-generated map products were in close agreement with the detailed soil survey of the area. The difference in spectral values appears to be due to a combination of subtle soil properties and crop growth patterns resulting from the different soil properties. Bands 4 (0.76-.90 micron), 5 (1.55-1.75 micron), and 7 (2.08-2.35 micron) were found to be responding to the within-field soil variability even with increasing ground cover. While these results are preliminary, they do indicate that the soil influence on the vegetation is being detected by TM and should provide improved information relating to crop and soil properties.

Study of spectral/radiometric characteristics of the Thematic Mapper for land use applications

NASA Technical Reports Server (NTRS)

Malila, W. A.; Metzler, M. D. (Principal Investigator)

1985-01-01

Progress during ERIM's tenth quarter of effort under the LANDSAT-4 and 5 Image Data Quality Assessment program for the Thematic Mapper is described. Coincident LANDSAT-4 and 5 fully corrected (CCT-PT) TM data are analyzed in more detail and revised band-by-band relationships between the two sensors derived. An analysis technique employing the matching of cumulative distributions is developed and used and is believed to offer advantages over the histogram matching procedure currently used to produce LANDSAT data. Multiplicative factors ranging from 0.987 to 1.145 and offsets ranging from -2.7 to -6.2 video quantum levels are required to cause LANDSAT-5 data to match LANDSAT-4 data values. Evidence of low level clipping is found in TM Bands 5 and 7 of LANDSAT-5 but not LANDSAT-4. Analysis of the information content of LANDSAT TM and MSS data is continued. Components of information loss are identified and quantified and the effects of coarsened quantization are explored.

Targeting of GLUT1-GLUT5 chimeric proteins in the polarized cell line Caco-2.

PubMed

Inukai, K; Takata, K; Asano, T; Katagiri, H; Ishihara, H; Nakazaki, M; Fukushima, Y; Yazaki, Y; Kikuchi, M; Oka, Y

1997-04-01

Caco-2, a human differentiated intestinal epithelial cell line, is a promising model for investigating the mechanism of polarized targeting of apical and basolateral membrane proteins. We stably transfected rat GLUT5 cDNA and rabbit GLUT1 cDNA into Caco-2 cells with an expression vector. Immunohistochemical study revealed that the GLUT5 protein expressed was localized at apical membranes and that the GLUT1 expressed was present primarily in the basolateral membranes of cells grown on permeable support. Next, to investigate the domain responsible for determining apical vs. basolateral sorting in glucose transporters, we prepared several GLUT1-GLUT5 chimeric cDNAs and transfected them into Caco-2 cells. A GLUT1 [N terminus approximately sixth transmembrane domain (TM6)]-GLUT5 [intracellular loop (IL) approximately C terminus] chimera was observed exclusively at the apical membrane, while GLUT1 (N terminus approximately IL)-GLUT5 (TM7 approximately C terminus) and GLUT1 (N terminus approximately TM12)-GLUT5 (C-terminal domain) chimeras were observed mainly at the basolateral membrane, a localization similar to that of GLUT1. Moreover, using a recombinant adenovirus expression system, we expressed a GLUT5 (N terminus approximately TM6)-GLUT1(IL)-GLUT5(TM7 approximately C-terminus) chimera, which was observed at the basolateral membrane. Based on these results, the C-terminal domain does not determine isoform-specific targeting of GLUT1 and GLUT5. Rather, it is the intracellular loop in glucose transporters that appears to play a pivotal role in apical-basolateral sorting signals in Caco-2 cells.

Mycobacterium-Inducible Nramp in Striped Bass (Morone saxatilis)

USGS Publications Warehouse

Burge, E.J.; Gauthier, David T.; Ottinger, C.A.; Van Veld, P.A.

2004-01-01

In mammals, the natural resistance-associated macrophage protein 1 gene, Nramp1, plays a major role in resistance to mycobacterial infections. Chesapeake Bay striped bass (Morone saxatilis) is currently experiencing an epizootic of mycobacteriosis that threatens the health of this ecologically and economically important species. In the present study, we characterized an Nramp gene in this species and obtained evidence that there is induction following Mycobacterium exposure. The striped bass Nramp gene (MsNramp) and a 554-amino-acid sequence contain all the signal features of the Nramp family, including a topology of 12 transmembrane domains (TM), the transport protein-specific binding-protein-dependent transport system inner membrane component signature, three N-linked glycosylation sites between TM 7 and TM 8, sites of casein kinase and protein kinase C phosphorylation in the amino and carboxy termini, and a tyrosine kinase phosphorylation site between TM 6 and TM 7. Phylogenetic analysis most closely grouped MsNramp with other teleost Nramp genes and revealed high sequence similarity with mammalian Nramp2. MsNramp expression was present in all tissues assayed by reverse transcription-PCR. Within 1 day of injection of Mycobacterium marinum, MsNramp expression was highly induced (17-fold higher) in peritoneal exudate (PE) cells compared to the expression in controls. The levels of MsNramp were three- and sixfold higher on days 3 and 15, respectively. Injection of Mycobacterium shottsii resulted in two-, five-, and threefold increases in gene expression in PE cells over the time course. This report is the first report of induction of an Nramp gene by mycobacteria in a poikilothermic vertebrate.

Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri.

PubMed

Stasiuk, Susan J; Scott, Maxwell J; Grant, Warwick N

2012-01-03

Parasitism is an important life history strategy in many metazoan taxa. This is particularly true of the Phylum Nematoda, in which parasitism has evolved independently at least nine times. The apparent ease with which parasitism has evolved amongst nematodes may, in part, be due to a feature of nematode development acting as a pre-adaptation for the transition from a free-living to a parasitic life history. One candidate pre-adaptive feature for evolution in terrestrial nematodes is the dauer larva, a developmentally arrested morph formed in response to environmental signals. We investigated the role of dauer development in the nematode, Parastrongyloides trichosuri, which has retained a complete free-living life cycle in addition to a life cycle as a mammalian gastrointestinal parasite. We show that the developmental switch between these life histories is sensitive to the same environmental cues as dauer arrest in free-living nematodes, including sensitivity to a chemical cue produced by the free-living stages. Furthermore, we show that genetic variation for the sensitivity of the cue(s) exists in natural populations of P. trichosuri, such that we derived inbred lines that were largely insensitive to the cue and other lines that were supersensitive to the cue. For this parasitic clade, and perhaps more widely in the phylum, the evolution of parasitism co-opted the dauer switch of a free-living ancestor. This lends direct support to the hypothesis that the switch to developmental arrest in the dauer larva acted as a pre-adaptation for the evolution of parasitism, and suggests that the sensory transduction machinery downstream of the cue may have been similarly co-opted and modified.

Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri

PubMed Central

2012-01-01

Background Parasitism is an important life history strategy in many metazoan taxa. This is particularly true of the Phylum Nematoda, in which parasitism has evolved independently at least nine times. The apparent ease with which parasitism has evolved amongst nematodes may, in part, be due to a feature of nematode development acting as a pre-adaptation for the transition from a free-living to a parasitic life history. One candidate pre-adaptive feature for evolution in terrestrial nematodes is the dauer larva, a developmentally arrested morph formed in response to environmental signals. Results We investigated the role of dauer development in the nematode, Parastrongyloides trichosuri, which has retained a complete free-living life cycle in addition to a life cycle as a mammalian gastrointestinal parasite. We show that the developmental switch between these life histories is sensitive to the same environmental cues as dauer arrest in free-living nematodes, including sensitivity to a chemical cue produced by the free-living stages. Furthermore, we show that genetic variation for the sensitivity of the cue(s) exists in natural populations of P. trichosuri, such that we derived inbred lines that were largely insensitive to the cue and other lines that were supersensitive to the cue. Conclusions For this parasitic clade, and perhaps more widely in the phylum, the evolution of parasitism co-opted the dauer switch of a free-living ancestor. This lends direct support to the hypothesis that the switch to developmental arrest in the dauer larva acted as a pre-adaptation for the evolution of parasitism, and suggests that the sensory transduction machinery downstream of the cue may have been similarly co-opted and modified. PMID:22214222

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

PubMed Central

Nelson, William C.; Stegen, James C.

2015-01-01

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum. PMID:26257709

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

DOE PAGES

Nelson, William C.; Stegen, James C.

2015-07-21

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesismore » of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.« less

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

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

Nelson, William C.; Stegen, James C.

2015-07-21

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. ‘Housekeeping’ genes and genes for biosynthesis ofmore » peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.« less

Single-cell genomics reveals co-metabolic interactions within uncultivated Marine Group A bacteria

NASA Astrophysics Data System (ADS)

Hawley, A. K.; Hallam, S. J.

2016-02-01

Marine Group A (MGA) bacteria represent a ubiquitous and abundant candidate phylum enriched in oxygen minimum zones (OMZs) and the deep ocean. Despite MGA prevalence little is known about their ecology and biogeochemistry. Here we chart the metabolic potential of 26 MGA single-cell amplified genomes sourced from different environments spanning ecothermodynamic gradients including open ocean waters, OMZs and methanogenic environments including a terephthalate-degrading bioreactor. Metagenomic contig recruitment to SAGs combined with tetra-nucleotide frequency distribution patterns resolved nine MGA population genome bins. All population genomes exhibited genomic streamlining with open ocean MGA being the most reduced. Different strategies for carbohydrate utilization, carbon fixation energy metabolism and respiratory pathways were identified between population genome bins, including various roles in the nitrogen and sulfur cycles. MGA inhabiting OMZ oxyclines encoded genes for partial denitrification with potential to feed into anammox and nitrification as well as a polysulfide reductase with a potential role in the cryptic sulfur cycle. MGA inhabiting anoxic waters, encoded NiFe hydrogenase and nitrous oxide reductase with the potential to complete partial denitrification pathways previously linked to sulfur oxidation in SUP05 bacteria. MGA from methanogenic environments encoded genes mediating cascading syntrophic interactions with fatty acid degraders and methanogens including reverse electron transport potential. The MGA phylum appears to have evolved alternative metabolic innovations adapting specific subgroups to occupy specific niches along ecothermodynamic gradients. Additionally, expression of MGA genes from different OMZ environments supports that these subgroups manifest an increasing propensity for co-metabolic interactions under energy limiting conditions that mandates a cooperative mode of existence with important implications for C, N and S cycling in marine ecosystems.

Pneumatic low-coherence interferometry otoscope to quantify tympanic membrane mobility and middle ear pressure.

PubMed

Won, Jungeun; Monroy, Guillermo L; Huang, Pin-Chieh; Dsouza, Roshan; Hill, Malcolm C; Novak, Michael A; Porter, Ryan G; Chaney, Eric; Barkalifa, Ronit; Boppart, Stephen A

2018-02-01

Pneumatic otoscopy to assess the mobility of the tympanic membrane (TM) is a highly recommended diagnostic method of otitis media (OM), a widespread middle ear infection characterized by the fluid accumulation in the middle ear. Nonetheless, limited depth perception and subjective interpretation of small TM displacements have challenged the appropriate and efficient examination of TM dynamics experienced during OM. In this paper, a pneumatic otoscope integrated with low coherence interferometry (LCI) was adapted with a controlled pressure-generating system to record the pneumatic response of the TM and to estimate middle ear pressure (MEP). Forty-two ears diagnosed as normal (n = 25), with OM (n = 10), or associated with an upper respiratory infection (URI) (n = 7) were imaged with a pneumatic LCI otoscope with an axial, transverse, and temporal resolution of 6 µm, 20 µm, and 1 msec, respectively. The TM displacement under pneumatic pressure transients (a duration of 0.5 sec with an intensity of ± 150 daPa) was measured to compute two metrics (compliance and amplitude ratio). These metrics were correlated with peak acoustic admittance and MEP from tympanometry and statistically compared via Welch's t- test. As a result, the compliance represents pneumatic TM mobility, and the amplitude ratio estimates MEP. The presence of a middle ear effusion (MEE) significantly decreased compliance (p<0.001). The amplitude ratio of the OM group was statistically less than that of the normal group (p<0.01), indicating positive MEP. Unlike tympanometry, pneumatic LCI otoscopy quantifies TM mobility as well as MEP regardless of MEE presence. With combined benefits of pneumatic otoscopy and tympanometry, pneumatic LCI otoscopy may provide new quantitative metrics for understanding TM dynamics and diagnosing OM.

Pneumatic low-coherence interferometry otoscope to quantify tympanic membrane mobility and middle ear pressure

PubMed Central

Won, Jungeun; Monroy, Guillermo L.; Huang, Pin-Chieh; Dsouza, Roshan; Hill, Malcolm C.; Novak, Michael A.; Porter, Ryan G.; Chaney, Eric; Barkalifa, Ronit; Boppart, Stephen A.

2018-01-01

Pneumatic otoscopy to assess the mobility of the tympanic membrane (TM) is a highly recommended diagnostic method of otitis media (OM), a widespread middle ear infection characterized by the fluid accumulation in the middle ear. Nonetheless, limited depth perception and subjective interpretation of small TM displacements have challenged the appropriate and efficient examination of TM dynamics experienced during OM. In this paper, a pneumatic otoscope integrated with low coherence interferometry (LCI) was adapted with a controlled pressure-generating system to record the pneumatic response of the TM and to estimate middle ear pressure (MEP). Forty-two ears diagnosed as normal (n = 25), with OM (n = 10), or associated with an upper respiratory infection (URI) (n = 7) were imaged with a pneumatic LCI otoscope with an axial, transverse, and temporal resolution of 6 µm, 20 µm, and 1 msec, respectively. The TM displacement under pneumatic pressure transients (a duration of 0.5 sec with an intensity of ± 150 daPa) was measured to compute two metrics (compliance and amplitude ratio). These metrics were correlated with peak acoustic admittance and MEP from tympanometry and statistically compared via Welch’s t-test. As a result, the compliance represents pneumatic TM mobility, and the amplitude ratio estimates MEP. The presence of a middle ear effusion (MEE) significantly decreased compliance (p<0.001). The amplitude ratio of the OM group was statistically less than that of the normal group (p<0.01), indicating positive MEP. Unlike tympanometry, pneumatic LCI otoscopy quantifies TM mobility as well as MEP regardless of MEE presence. With combined benefits of pneumatic otoscopy and tympanometry, pneumatic LCI otoscopy may provide new quantitative metrics for understanding TM dynamics and diagnosing OM. PMID:29552381

Initiation of Levodopa-Carbidopa Intestinal Gel Infusion Using Telemedicine (Video Communication System) Facilitates Efficient and Well-Accepted Home Titration in Patients with Advanced Parkinson's Disease.

PubMed

Willows, Thomas; Dizdar, Nil; Nyholm, Dag; Widner, Håkan; Grenholm, Peter; Schmiauke, Ursula; Urbom, Anna; Groth, Kristina; Larsson, Jörgen; Permert, Johan; Kjellander, Susanna

2017-01-01

Levodopa-carbidopa intestinal gel (LCIG; Duodopa®) is used for continuous infusion in advanced Parkinson's disease. To achieve optimal effect, the LCIG dose is individually titrated, traditionally conducted during hospitalization in Sweden. However, dose adjustment depends on surrounding conditions, physical activity, and emotional stress, which is why titration at home could be beneficial. Telemedicine (TM) using a video communication system offers alternative titration procedures, allowing LCIG initiation at home. Study objectives were to show the feasibility of TM for LCIG home titration, evaluate resource use, and assess patient, neurologist, and nurse satisfaction. Four clinics enrolled 15 patients to observe efficiency and feasibility of TM-based monitoring. Patient median (range) age was 67 (52-73) years and time since diagnosis was 10 (7-23) years. Median time between LCIG initiation and end of TM-assisted titration was 2.8 (2.0-13.8) days. Median time required for home titration by neurologists, nurses, and patients was (hours:minutes) 1 : 14 (0 : 29-1 : 52), 5 : 49 (2 : 46-10 : 3), and 8 : 53 (4 : 11-14 : 11), respectively. Neurologists and nurses considered this to be less time than required for hospital titration. TM allowed patients 92% free time from start to end of titration. Technical problems associated with TM contacts were rare, mostly related to digital link, and quickly resolved. Patients, neurologists, and nurses were satisfied using TM. No serious adverse events were reported; there was one device complaint (tube occlusion). In this study, TM-assisted LCIG titration at home was resource-efficient, technically feasible, well-accepted and was deemed satisfactory by patients, neurologists, and nurses.

Early thrombomodulin-α administration outcome for acute disseminated intravascular coagulopathy in gastrointestinal surgery.

PubMed

Konishi, Hirotaka; Okamoto, Kazuma; Shoda, Katsutoshi; Arita, Tomohiro; Kosuga, Toshiyuki; Morimura, Ryo; Komatsu, Shuhei; Murayama, Yasutoshi; Shiozaki, Atsushi; Kuriu, Yoshiaki; Ikoma, Hisashi; Nakanishi, Masayoshi; Ichikawa, Daisuke; Fujiwara, Hitoshi; Otsuji, Eigo

2017-02-07

To investigate the efficacy of thrombomodulin (TM)-α for treatment of disseminated intravascular coagulopathy (DIC) in the field of gastrointestinal surgery. Thirty-six peri-operative DIC patients in the field of gastrointestinal surgery who were treated with TM-α were retrospectively investigated. The relationships between patient demographics and the efficacy of TM-α were examined. Analysis of survival at 28 d was also performed on some parameters by means of the Kaplan-Meier method. Relationships between the initiation of TM-α and patient demographics were also evaluated. Abscess formation or bacteremia was the most frequent cause of DIC (33%), followed by digestive tract perforation (31%). Twenty-six patients developed DIC after surgery, frequently within 1 wk (81%). TM-α was most often administered within 1 d of the DIC diagnosis (72%) and was continued for more than 3 d (64%). Although bleeding tendency was observed in 7 patients (19%), a hemostatic procedure was not needed. DIC scores, systemic inflammatory response syndrome (SIRS) scores, quick-sequential organ failure assessment (qSOFA) scores, platelet counts, and prothrombin time ratios significantly improved after 1 wk ( P < 0.05, for all). The overall survival rate at 28 d was 71%. The duration of TM-α administration (≥ 4 , ≤ 6) and improvements in DIC-associated scores (DIC, SIRS and qSOFA) at 1 wk were significantly better prognostic factors for 28-d survival ( P < 0.05, for all). TM-α was administered significantly earlier to patients with severe clinical symptoms, such as high qSOFA scores, sepsis, shock or high lactate values ( P < 0.05, for all). Early administration of TM-α and improvements in each parameter were essential for treatment of DIC. The diagnosis of patients with mild symptoms requires further study.

Graphene as a nanocarrier for tamoxifen induces apoptosis in transformed cancer cell lines of different origins.

PubMed

Misra, Santosh K; Kondaiah, Paturu; Bhattacharya, Santanu; Rao, C N R

2012-01-09

A cationic amphiphile, cholest-5en-3β-oxyethyl pyridinium bromide (PY(+) -Chol), is able to efficiently disperse exfoliated graphene (GR) in water by the physical adsorption of PY(+) -Chol on the surface of GR to form stable, dark aqueous suspensions at room temperature. The GR-PY(+) -Chol suspension can then be used to solubilize Tamoxifen Citrate (TmC), a breast cancer drug, in water. The resulting TmC-GR-PY(+) -Chol is stable for a long time without any precipitation. Fluorescence emission and UV absorption spectra indicate the existence of noncovalent interactions between TmC, GR, and PY(+) -Chol in these suspensions. Electron microscopy shows the existence of segregated GR sheets and TmC 'ribbons' in the composite suspensions. Atomic force microscopy indicates the presence of 'extended' structures of GR-PY(+) -Chol, which grows wider in the presence of TmC. The slow time-dependent release of TmC is noticed in a reconstituted cell culture medium, a property useful as a drug carrier. TmC-GR-PY(+) -Chol selectively enhanced the cell death (apoptosis) of the transformed cancer cells compared to normal cells. This potency is found to be true for a wide range of transformed cancer cells viz. HeLa, A549, ras oncogene-transformed NIH3T3, HepG2, MDA-MB231, MCF-7, and HEK293T compared to the normal cell HEK293 in vitro. Confocal microscopy confirmed the high efficiency of TmC-GR-PY(+) -Chol in delivering the drug to the cells, compared to the suspensions devoid of GR. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gene structure, cDNA characterization and RNAi-based functional analysis of a myeloid differentiation factor 88 homolog in Tenebrio molitor larvae exposed to Staphylococcus aureus infection.

PubMed

Patnaik, Bharat Bhusan; Patnaik, Hongray Howrelia; Seo, Gi Won; Jo, Yong Hun; Lee, Yong Seok; Lee, Bok Luel; Han, Yeon Soo

2014-10-01

Myeloid differentiation factor 88 (MyD88), an intracellular adaptor protein involved in Toll/Toll-like receptor (TLR) signal processing, triggers activation of nuclear factor-kappaB (NF-κB) transcription factors. In the present study, we analyzed the gene structure and biological function of MyD88 in a coleopteran insect, Tenebrio molitor (TmMyD88). The TmMyD88 gene was 1380 bp in length and consisted of five exons and four introns. The 5'-flanking sequence revealed several putative transcription factor binding sites, such as STAT-4, AP-1, cJun, cfos, NF-1 and many heat shock factor binding elements. The cDNA contained a typical death domain, a conservative Toll-like interleukin-1 receptor (TIR) domain, and a C-terminal extension (CTE). The TmMyD88 TIR domain showed three significantly conserved motifs for interacting with the TIR domain of TLRs. TmMyD88 was grouped within the invertebrate cluster of the phylogenetic tree and shared 75% sequence identity with the TIR domain of Tribolium castaneum MyD88. Homology modeling of the TmMyD88 TIR domain revealed five parallel β-strands surrounded by five α-helices that adopted loop conformations to function as an adaptor. TmMyD88 expression was upregulated 7.3- and 4.79-fold after 12 and 6h, respectively, of challenge with Staphylococcus aureus and fungal β-1,3 glucan. Silencing of the TmMyD88 transcript by RNA interference led to reduced resistance of the host to infection by S. aureus. These results indicate that TmMyD88 is required for survival against Staphylococcus infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows

PubMed Central

Opdahl, Lee James; Gonda, Michael G.

2018-01-01

The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides. PMID:29495256

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows.

PubMed

Opdahl, Lee James; Gonda, Michael G; St-Pierre, Benoit

2018-02-24

The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6-50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers ( Ruminococcus flavefaciens and Fibrobacter succinogenes ), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides.

The split portal: Description of a new accessory posterior portal for arthroscopic shoulder instability procedures.

PubMed

Mirouse, Guillaume; Nourissat, Geoffroy

2016-02-01

Open approach to the posterior shoulder during bone block for posterior shoulder instability is challenging. Anatomical study was performed to identify landmarks of a portal, avoiding soft tissue damage, between the infraspinatus (IS) and teres minor (TM) muscles and distant from the supra-scapular nerve (SSN) for arthroscopic shoulder bone block. Eight fresh-frozen cadaveric shoulder specimens were used. The arthroscope was introduced through the soft point (SP). A guide wire was placed through the SP, in the rotator interval direction. A posterior open dissection exposed the split between the IS and TM. A new guide wire was placed into the split, parallel to the first wire, to locate the new posterior arthroscopic approach. Ten distances were measured to define the safe position. The mean values were: SP to split IS-TM: 2 ± 0.2 (2-2.8); spinal bone to split IS-TM: 5 ± 0.5 (3-6.2); split IS-TM to posterior glenoid 6 o'clock: 1.3 ± 0.3 (0.6-1.6), 9 o'clock: 1.5 ± 0.3 (1-1.9), and 12 o'clock: 2 ± 0.1 (2.1-2.4); SSN to posterior glenoid 6 o'clock: 2.4 ± 0.2 (2.1-2.6), 9 o'clock: 1.7 ± 0.1 (1.5-1.8), and 12 o'clock: 1.5 ± 0.3 (1.2-2.1); and SSN to split IS-TM: 2 ± 0.3 (1.2-2.1). This preliminary anatomical study described a posterior arthroscopic portal located 2 cm under the SP, parallel to the SP portal direction, and finishing between 7 and 8 o'clock at the posterior rim of the glenoid. For arthroscopic shoulder bone block, this portal can avoid muscle and SSN lesions.

Histopathology of tympanic membranes from patients with ventilation tubes.

PubMed

Oktay, Mehmet Faruk; Tansuker, Hasan Deniz; Fukushima, Hisaki; Paparella, Michael M; Schachern, Patricia A; Cureoglu, Sebahattin

2018-06-01

To evaluate the histopathologic changes in tympanic membranes (TMs) with ventilation tubes (VTs). In this retrospective human temporal bone study our overall study group included 4 subgroups of TMs from deceased donors as follows: 24 with a history of VT insertion for chronic otitis media with effusion (COME-VT); 5 with a history of VT insertion for Meniere's disease (MD-VT); 33 without a history of VT insertion for chronic otitis media with effusion (COME); and 14 without a history of VT insertion for Meniere's disease (MD). We classified the extent of migration of the outer keratinized squamous epithelium onto the inner surface of TM perforations and noted the presence and location of tympanosclerosis, of atrophy, of perforation, and/or of cholesteatoma formation. Tympanosclerosis occurred in 14/24 TMs in the COME-VT subgroup; 2/5, MD-VT; 7/33, COME; and 0/14, MD. The VT insertion site was mostly in the anteroinferior (63%) quadrant of the TM; tympanosclerosis occurred more frequently in the posteroinferior (42%) and posterosuperior (33%) quadrants. We found no significant correlation between the location of tympanosclerosis and the VT insertion site (P>0.05). Atrophy occurred in 7/24 TMs in the COME-VT subgroup; 3/5, MD-VT; 8/33, COME; and 2/14, MD. We found no significant correlation between the location of atrophy and the VT insertion site; however, atrophy was located mostly in the anteroinferior quadrant (one of the most common VT insertion sites) of the TM. Regarding the ingrowth of keratinized epithelium, the mucocutanous junction was detected at any point at the inner surface of the TM in 50% of the specimens. We observed intratympanic cholesteatoma formation in 2/24 TMs in the COME-VT subgroup. TM changes due to VT insertion are more common than previously realized. Meticulous otomicroscopic evaluation of the TM is necessary during tympanomastoidectomies in order to prevent the intratympanic inclusion pearls and squamous epithelial ingrowth to prevent any further cholesteatoma formation. Copyright © 2017. Published by Elsevier B.V.

Delineation of the Caffeine C-8 Oxidation Pathway in Pseudomonas sp. Strain CBB1 via Characterization of a New Trimethyluric Acid Monooxygenase and Genes Involved in Trimethyluric Acid Metabolism

PubMed Central

Mohanty, Sujit Kumar; Yu, Chi-Li; Das, Shuvendu; Louie, Tai Man; Gakhar, Lokesh

2012-01-01

The molecular basis of the ability of bacteria to live on caffeine via the C-8 oxidation pathway is unknown. The first step of this pathway, caffeine to trimethyluric acid (TMU), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. Here, we report the detailed characterization of the second enzyme, a novel NADH-dependent trimethyluric acid monooxygenase (TmuM), a flavoprotein that catalyzes the conversion of TMU to 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU). This product spontaneously decomposes to racemic 3,6,8-trimethylallantoin (TMA). TmuM prefers trimethyluric acids and, to a lesser extent, dimethyluric acids as substrates, but it exhibits no activity on uric acid. Homology models of TmuM against uric acid oxidase HpxO (which catalyzes uric acid to 5-hydroxyisourate) reveal a much bigger and hydrophobic cavity to accommodate the larger substrates. Genes involved in the caffeine C-8 oxidation pathway are located in a 25.2-kb genomic DNA fragment of CBB1, including cdhABC (coding for caffeine dehydrogenase) and tmuM (coding for TmuM). Comparison of this gene cluster to the uric acid-metabolizing gene cluster and pathway of Klebsiella pneumoniae revealed two major open reading frames coding for the conversion of TM-HIU to S-(+)-trimethylallantoin [S-(+)-TMA]. The first one, designated tmuH, codes for a putative TM-HIU hydrolase, which catalyzes the conversion of TM-HIU to 3,6,8-trimethyl-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (TM-OHCU). The second one, designated tmuD, codes for a putative TM-OHCU decarboxylase which catalyzes the conversion of TM-OHCU to S-(+)-TMA. Based on a combination of enzymology and gene-analysis, a new degradative pathway for caffeine has been proposed via TMU, TM-HIU, TM-OHCU to S-(+)-TMA. PMID:22609920

Signal Processing in Reverberation- A Summary of Performance Capability

DTIC Science & Technology

1972-08-30

34 LkP+52-DOGLB. UNCLASSIFIED N, TM No. TC- 173-72 LC INAVAL UNDERWATER SYSTEMS CENTER Technical Memorandum SIGNAL PROCESSING IN REVERBERATION- A...SUMMARY OF PERFORMANCE CAPABILITY Date: 30 August 1972 Prepared by: -- v i Alert H. Nuttall Office of the Director of Science and Technology 2TICELECTEI...Nuffall Office of the Director of Science and Technology Approved for public release; distribution unlimited UNCLASSIFIED TM No. TC- I7P-72 NAVAL

Analyzing Landsat time-series data across adjacent path/rows and across multiple cycles of FIA: Lessons learned in southern Missouri

Treesearch

Mark Nelson; Sean Healey; W. Keith Moser; Mark Hansen; Warren Cohen; Mark Hatfield; Nancy Thomas; Jeff Masek

2009-01-01

The North American Forest Dynamics (NAFD) Program is assessing disturbance and regrowth in the forests of the continent. These forest dynamics are interpreted from per-pixel estimates of forest biomass, which are produced for a time series of Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced TM Plus images. Image data are combined with sample plot data from the...

Post-marketing monitoring of intussusception after rotavirus vaccination in Japan.

PubMed

Bauchau, Vincent; Van Holle, Lionel; Mahaux, Olivia; Holl, Katsiaryna; Sugiyama, Keiji; Buyse, Hubert

2015-07-01

Rotarix(TM) was launched in November 2011 in Japan to prevent rotavirus gastroenteritis. Some studies suggest that Rotarix(TM) may have a temporal association with a risk of intussusception (IS). We assessed a possible association between IS and Rotarix(TM) vaccination in Japan. All IS cases spontaneously reported post-vaccination (Brighton collaboration levels 1, 2, and 3) were extracted from the GlaxoSmithKline spontaneous report database on the 11th of January 2013. Expected numbers of IS cases were estimated using the number of vaccine doses distributed and the Japanese incidence rate of IS stratified by month of age. The observed versus expected analysis considered the IS cases for each risk period (7 and 30 days post-vaccination) and for each vaccine dose (two doses). Before January 2013, approximately 601 000 Rotarix(TM) doses were distributed in Japan. For a risk period of 7 days post-dose 1 and post-dose 2, 10 and five IS cases were observed, whereas 3.4 and 7.6 were expected, providing an observed-to-expected ratio of 2.96 (95% confidence interval [CI]: 1.42; 5.45) and 0.66 (95% CI: 0.21; 1.53), respectively. For a risk period of 30 days post-dose 1 and post-dose 2, 14 and eight cases were observed, whereas 14.5 and 32.7 were expected, providing an observed-to-expected ratio of 0.97 (95% CI: 0.53; 1.62) and 0.24 (95% CI: 0.11; 0.48), respectively. A statistically significant excess of IS cases was observed within 7 days post-dose 1, but not post-dose 2. These results are consistent with previous observations in large post-marketing safety studies in other world regions. © 2015 The Authors. Pharmacoepidemiology and Drug Safety published by John Wiley & Sons, Ltd.

Post‐marketing monitoring of intussusception after rotavirus vaccination in Japan†

PubMed Central

Bauchau, Vincent; Van Holle, Lionel; Mahaux, Olivia; Holl, Katsiaryna; Sugiyama, Keiji

2015-01-01

Abstract Purpose Rotarix TM was launched in November 2011 in Japan to prevent rotavirus gastroenteritis. Some studies suggest that Rotarix TM may have a temporal association with a risk of intussusception (IS). We assessed a possible association between IS and Rotarix TM vaccination in Japan. Methods All IS cases spontaneously reported post‐vaccination (Brighton collaboration levels 1, 2, and 3) were extracted from the GlaxoSmithKline spontaneous report database on the 11th of January 2013. Expected numbers of IS cases were estimated using the number of vaccine doses distributed and the Japanese incidence rate of IS stratified by month of age. The observed versus expected analysis considered the IS cases for each risk period (7 and 30 days post‐vaccination) and for each vaccine dose (two doses). Results Before January 2013, approximately 601 000 Rotarix TM doses were distributed in Japan. For a risk period of 7 days post‐dose 1 and post‐dose 2, 10 and five IS cases were observed, whereas 3.4 and 7.6 were expected, providing an observed‐to‐expected ratio of 2.96 (95% confidence interval [CI]: 1.42; 5.45) and 0.66 (95% CI: 0.21; 1.53), respectively. For a risk period of 30 days post‐dose 1 and post‐dose 2, 14 and eight cases were observed, whereas 14.5 and 32.7 were expected, providing an observed‐to‐expected ratio of 0.97 (95% CI: 0.53; 1.62) and 0.24 (95% CI: 0.11; 0.48), respectively. Conclusion A statistically significant excess of IS cases was observed within 7 days post‐dose 1, but not post‐dose 2. These results are consistent with previous observations in large post‐marketing safety studies in other world regions. © 2015 The Authors. Pharmacoepidemiology and Drug Safety published by John Wiley & Sons, Ltd. PMID:26013569

Capillary electrophoretic analysis of synthetic short-chain oligoribonucleotides.

PubMed

Cellai, L; Onori, A M; Desiderio, C; Fanali, S

1998-12-01

Thirty synthetic oligoribonucleotides, 3 to 18 nucleotides (nt) long, were analyzed by capillary electrophoresis, under nondenaturing conditions, using a commercial kit. The migration time t(m) was dependent on nt length and composition, capillary length, operating temperature, and type of sieving polymer. Under fixed experimental conditions, the t(m) proved predictable by the equation: t(m) = [0.22(n-1) + 6.14A/n + 6.86G/n + 3.61 (C+U)/n] min, for n>3, where A/n, G/n, C/n, U/n is the frequency of each type of nt within the oligonucleotide (ONT). The equation accounts for the influence of charge-to-mass ratio on t(m), but not for structural effects, if present. This approximation is acceptable for short ONTs. The possibility of detecting n+1, n-1, n-2 impurities, having predicted the t(m), is of crucial importance in assessing the purity of synthetic ONTs dedicated to structural studies. This appears to be feasible. High resolution was shown among homologous series of ONTs of increasing length, and in some cases, even within groups of ONTs of the same length but different composition. The addition of 7 M urea to the buffer, as denaturing agent, accelerates the t(m) and significantly lowers the resolution for the shortest ONTs. It was also possible to monitor the state of association of mixtures of RNA and DNA sequence-complementary strands.

Optical spectroscopy of lanthanide ions in ZnO-TeO2 glasses.

PubMed

Rolli, R; Wachtler, K; Wachtler, M; Bettinelli, M; Speghini, A; Ajò, D

2001-09-01

Zinc tellurite glasses of compositions 19ZnO-80TeO2-1Ln2O3 with Ln = Eu, Er, Nd and Tm were prepared by melt quenching. The absorption spectra were measured and from the experimental oscillator strengths of the f-->f transitions the Judd-Ofelt parameters ohm(lambda) were obtained. The values of the ohm(lambda) parameters are in the range usually observed for oxide glasses. For Nd3+ and Er3+, luminescence spectra in the near infrared were measured and the stimulated emission cross sections sigma(p) were evaluated for some laser transitions. The high values of sigma(p), especially for Nd3+, make them possible candidates for optical applications. Fluorescence line narrowing (FLN) spectra of the Eu3+ doped glass were measured at 20 K, and the energies of the Stark components of the 7F1 and 7F2 states were obtained. A crystal field analysis was carried out assuming a C2v site symmetry. The behaviour of the crystal field ratios B22/B20 and B44/B40 agrees reasonably well with the values calculated using the geometric model proposed by Brecher and Riseberg. The crystal field strength at the Eu3+ sites appears to be very low compared to other oxide glasses.

Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

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

Riley, Robert; Salamov, Asaf; Otillar, Robert

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes revealsmore » that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.« less

Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica.

PubMed

Teixeira, Lia C R S; Peixoto, Raquel S; Cury, Juliano C; Sul, Woo Jun; Pellizari, Vivian H; Tiedje, James; Rosado, Alexandre S

2010-08-01

The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago.

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

PubMed Central

Gao, Beile

2012-01-01

Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

PubMed Central

Ferrari, Belinda C.; Binnerup, Svend J.; Gillings, Michael

2005-01-01

Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used. PMID:16332866

Post-marketing surveillance of thrombomodulin alfa, a novel treatment of disseminated intravascular coagulation - safety and efficacy in 1,032 patients with hematologic malignancy.

PubMed

Asakura, Hidesaku; Takahashi, Hoyu; Tsuji, Hajime; Matsushita, Tadashi; Ninomiya, Hideyuki; Honda, Goichi; Mimuro, Jun; Eguchi, Yutaka; Kitajima, Isao; Sakata, Yoichi

2014-03-01

Post-marketing surveillance of thrombomodulin alfa (TM-α) was performed to evaluate safety and efficacy in patients with disseminated intravascular coagulation (DIC) with hematologic malignancy. All patients treated with TM-α from May 2008 to April 2010 in Japan were included. Information about baseline characteristics, safety, and efficacy were collected. The DIC resolution rate, survival rate on Day 28 after the last TM-α administration, and changes in DIC score and coagulation tests were evaluated. The underlying diseases associated with DIC were acute myeloid leukemia (except for acute promyelocytic leukemia, n=350), lymphoma (n=199), acute promyelocytic leukemia (n=172), acute lymphoblastic leukemia (n=156), myelodysplastic syndromes (n=61), and other (n=94). The incidence rates of bleeding-related adverse events and adverse drug reactions were 17.8% and 4.6%, respectively. In subjects with bleeding symptoms at baseline, 55.0% were assessed as disappeared or improved based on symptoms after TM-α treatment. The DIC resolution and survival rates were 55.9% and 70.7%, respectively. The DIC score and coagulation tests including thrombin-antithrombin complex (TAT) were significantly improved. Coagulation tests were significantly improved after TM-α treatment even in subjects whose clinical course of underlying disease was assessed as unchanged or exacerbated. This surveillance confirmed the safety and efficacy of TM-α in clinical practice, thus TM-α may be an ideal treatment for patients with DIC based upon hematologic malignancy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Does the use of Nintendo Wii SportsTM improve arm function? Trial of WiiTM in Stroke: a randomized controlled trial and economics analysis.

PubMed

Adie, Katja; Schofield, Christine; Berrow, Margie; Wingham, Jennifer; Humfryes, John; Pritchard, Colin; James, Martin; Allison, Rhoda

2017-02-01

The Trial of Wii™ in Stroke investigated the efficacy of using the Nintendo Wii Sports™ (Wii TM ) to improve affected arm function after stroke. Multicentre, pragmatic, parallel group, randomized controlled trial. Home-based rehabilitation. A total of 240 participants aged 24-90 years with arm weakness following a stroke within the previous six months. Participants were randomly assigned to exercise daily for six weeks using the Wii TM or arm exercises at home. Primary outcome was change in the affected arm function at six weeks follow-up using the Action Research Arm Test. Secondary outcomes included occupational performance, quality of life, arm function at six months and a cost effectiveness analysis. The study was completed by 209 participants (87.1%). There was no significant difference in the primary outcome of affected arm function at six weeks follow-up (mean difference -1.7, 95% CI -3.9 to 0.5, p = 0.12) and no significant difference in secondary outcomes, including occupational performance, quality of life or arm function at six months, between the two groups. No serious adverse events related to the study treatment were reported. The cost effectiveness analysis showed that the Wii TM was more expensive than arm exercises £1106 (SD 1656) vs. £730 (SD 829) (probability 0.866). The trial showed that the Wii TM was not superior to arm exercises in home-based rehabilitation for stroke survivors with arm weakness. The Wii TM was well tolerated but more expensive than arm exercises.

TransMilenio, a Scalable Bus Rapid Transit System for Promoting Physical Activity.

PubMed

Lemoine, Pablo D; Sarmiento, Olga L; Pinzón, Jose David; Meisel, Jose D; Montes, Felipe; Hidalgo, Dario; Pratt, Michael; Zambrano, Juan Manuel; Cordovez, Juan Manuel; Zarama, Roberto

2016-04-01

Transport systems can play an important role in increasing physical activity (PA). Bogotá has been recognized for its bus rapid transit (BRT) system, TransMilenio (TM). To date, BRTs have been implemented in over 160 cities worldwide. The aim of this study was to assess the association between PA and the use of TM among adults in Bogotá. The study consists of a cross-sectional study conducted from 2010 to 2011 with 1000 adults. PA was measured using the International Physical Activity Questionnaire. In a subsample of 250 adults, PA was objectively measured using ActiGraph accelerometers. Analyses were conducted using multilevel logistic regression models. The use of TM was associated with meeting moderate-to-vigorous PA (MVPA). TM users were more likely to complete an average of >22 min a day of MVPA (odds ratio [OR] = 3.1, confidence interval [CI] = 95 % 1.4-7.1) and to walk for transportation for ≥150 min per week (OR = 1.5; CI = 95 % 1.1-2.0). The use of TM was associated with 12 or more minutes of MVPA (95 % CI 4.5-19.4, p < 0.0001). Associations between meeting PA recommendations and use of TM did not differ by socioeconomic status (p value = 0.106) or sex (p value = 0.288). The use of TM is a promising strategy for enhancing public health efforts to reduce physical inactivity through walking for transport. Given the expansion of BRTs, these results could inform the development of transport PA programs in low- to high-income countries.

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria)

PubMed Central

Bendiks, Zachary A.; Lang, Jenna M.; Darling, Aaron E.; Coil, David A.

2013-01-01

Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds). This strain was isolated from a residential toilet as part of an undergraduate student research project to sequence reference genomes of microbes from the built environment. PMID:23516225

Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study.

PubMed

Lindheim, Lisa; Bashir, Mina; Münzker, Julia; Trummer, Christian; Zachhuber, Verena; Leber, Bettina; Horvath, Angela; Pieber, Thomas R; Gorkiewicz, Gregor; Stadlbauer, Vanessa; Obermayer-Pietsch, Barbara

2017-01-01

Polycystic ovary syndrome (PCOS) is a common female endocrinopathy of unclear origin characterized by hyperandrogenism, oligo-/anovulation, and ovarian cysts. Women with PCOS frequently display overweight, insulin resistance, and systemic low-grade inflammation. We hypothesized that endotoxemia resulting from a leaky gut is associated with inflammation, insulin resistance, fat accumulation, and hyperandrogenemia in PCOS. In this pilot study, we compared the stool microbiome, gut permeability, and inflammatory status of women with PCOS and healthy controls. 16S rRNA gene amplicon sequencing was performed on stool samples from 24 PCOS patients and 19 healthy controls. Data processing and microbiome analysis were conducted in mothur and QIIME using different relative abundance cut-offs. Gut barrier integrity, endotoxemia, and inflammatory status were evaluated using serum and stool markers and associations with reproductive, metabolic, and anthropometric parameters were investigated. The stool microbiome of PCOS patients showed a lower diversity and an altered phylogenetic composition compared to controls. We did not observe significant differences in any taxa with a relative abundance>1%. When looking at rare taxa, the relative abundance of bacteria from the phylum Tenericutes, the order ML615J-28 (phylum Tenericutes) and the family S24-7 (phylum Bacteroidetes) was significantly lower and associated with reproductive parameters in PCOS patients. Patients showed alterations in some, but not all markers of gut barrier function and endotoxemia. Patients with PCOS have a lower diversity and an altered phylogenetic profile in their stool microbiome, which is associated with clinical parameters. Gut barrier dysfunction and endotoxemia were not driving factors in this patient cohort, but may contribute to the clinical phenotype in certain PCOS patients.

Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study

PubMed Central

Bashir, Mina; Münzker, Julia; Trummer, Christian; Zachhuber, Verena; Leber, Bettina; Horvath, Angela; Pieber, Thomas R.; Gorkiewicz, Gregor; Stadlbauer, Vanessa; Obermayer-Pietsch, Barbara

2017-01-01

Background Polycystic ovary syndrome (PCOS) is a common female endocrinopathy of unclear origin characterized by hyperandrogenism, oligo-/anovulation, and ovarian cysts. Women with PCOS frequently display overweight, insulin resistance, and systemic low-grade inflammation. We hypothesized that endotoxemia resulting from a leaky gut is associated with inflammation, insulin resistance, fat accumulation, and hyperandrogenemia in PCOS. In this pilot study, we compared the stool microbiome, gut permeability, and inflammatory status of women with PCOS and healthy controls. Methods 16S rRNA gene amplicon sequencing was performed on stool samples from 24 PCOS patients and 19 healthy controls. Data processing and microbiome analysis were conducted in mothur and QIIME using different relative abundance cut-offs. Gut barrier integrity, endotoxemia, and inflammatory status were evaluated using serum and stool markers and associations with reproductive, metabolic, and anthropometric parameters were investigated. Results The stool microbiome of PCOS patients showed a lower diversity and an altered phylogenetic composition compared to controls. We did not observe significant differences in any taxa with a relative abundance>1%. When looking at rare taxa, the relative abundance of bacteria from the phylum Tenericutes, the order ML615J-28 (phylum Tenericutes) and the family S24-7 (phylum Bacteroidetes) was significantly lower and associated with reproductive parameters in PCOS patients. Patients showed alterations in some, but not all markers of gut barrier function and endotoxemia. Conclusion Patients with PCOS have a lower diversity and an altered phylogenetic profile in their stool microbiome, which is associated with clinical parameters. Gut barrier dysfunction and endotoxemia were not driving factors in this patient cohort, but may contribute to the clinical phenotype in certain PCOS patients. PMID:28045919

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes

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

Hahnke, Richard L.; Stackebrandt, Erko; Meier-Kolthoff, Jan P.

Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2T and its next relatives seem more closely related to the genus Myroides than to the typemore » species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. In conclusion, based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.« less

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes

DOE PAGES

Hahnke, Richard L.; Stackebrandt, Erko; Meier-Kolthoff, Jan P.; ...

2015-07-30

Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2T and its next relatives seem more closely related to the genus Myroides than to the typemore » species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. In conclusion, based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.« less

Fisetin Protects PC12 Cells from Tunicamycin-Mediated Cell Death via Reactive Oxygen Species Scavenging and Modulation of Nrf2-Driven Gene Expression, SIRT1 and MAPK Signaling in PC12 Cells

PubMed Central

Yen, Jui-Hung; Wu, Pei-Shan; Chen, Shu-Fen; Wu, Ming-Jiuan

2017-01-01

Background: Fisetin (3,7,3′,4′-tetrahydroxyflavone) is a dietary flavonol and exhibits antioxidant, anti-inflammatory, and neuroprotective activities. However, high concentration of fisetin is reported to produce reactive oxygen species (ROS), induce endoplasmic reticulum (ER) stress and cause cytotoxicity in cancer cells. The aim of this study is to investigate the cytoprotective effects of low concentration of fisetin against tunicamycin (Tm)-mediated cytotoxicity in neuronal-like catecholaminergic PC12 cells. Methods: Cell viability was assayed by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and apoptotic and autophagic markers were analyzed by Western blot. Gene expression of unfolded protein response (UPR) and Phase II enzymes was further investigated using RT-Q-PCR or Western blotting. Intracellular ROS level was measured using 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA) by a fluorometer. The effects of fisetin on mitogen activated protein kinases (MAPKs) and SIRT1 (Sirtuin 1) signaling pathways were examined using Western blotting and specific inhibitors. Results: Fisetin (<20 µM) restored cell viability and repressed apoptosis, autophagy and ROS production in Tm-treated cells. Fisetin attenuated Tm-mediated expression of ER stress genes, such as glucose-regulated proteins 78 (GRP78), C/EBP homologous protein (CHOP also known as GADD153) and Tribbles homolog 3 (TRB3), but induced the expression of nuclear E2 related factor (Nrf)2-targeted heme oxygenase (HO)-1, glutamate cysteine ligase (GCL) and cystine/glutamate transporter (xCT/SLC7A11), in both the presence and absence of Tm. Moreover, fisetin enhanced phosphorylation of ERK (extracellular signal-regulated kinase), JNK (c-JUN NH2-terminal protein kinase), and p38 MAPK. Addition of JNK and p38 MAPK inhibitor significantly antagonized its cytoprotective activity and modulatory effects on UPR. Fisetin also restored Tm-inhibited SIRT1 expression and addition of sirtinol (SIRT1 activation inhibitor) significantly blocked fisetin-mediated cytoprotection. In conclusion, this result shows that fisetin activates Nrf2, MAPK and SIRT1, which may elicit adaptive cellular stress response pathways so as to protect cells from Tm-induced cytotoxicity. PMID:28420170

Thermodynamics for the Formation of Double-Stranded DNA-Single-Walled Carbon Nanotube Hybrids.

PubMed

Shiraki, Tomohiro; Tsuzuki, Akiko; Toshimitsu, Fumiyuki; Nakashima, Naotoshi

2016-03-24

For the first time, the thermodynamics are described for the formation of double-stranded DNA (ds-DNA)-single-walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds-DNAs d(A)20 -d(T)20 and nuclear factor (NF)-κB decoy. UV/Vis/near-IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single-stranded DNAs (ss-DNAs), including d(A)20 and d(T)20, are also used for comparison. The d(A)20-d(T)20 shows a drastic change in its thermodynamic parameters around the melting temperature (Tm ) of the DNA oligomer. No such Tm dependency was measured, owing to high Tm in the NF-κB decoy DNA and no Tm in the ss-DNA. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of LANDSAT-D thematic mapper performance as applied to hydrocarbon exploration

NASA Technical Reports Server (NTRS)

Everett, J. R. (Principal Investigator)

1983-01-01

Two fully processed test tapes were enhanced and evaluated at scales up to 1:10,000, using both hardcopy output and interactive screen display. A large scale, the Detroit, Michigan scene shows evidence of an along line data slip every sixteenth line in TM channel 2. Very large scale products generated in false color using channels 1,3, and 4 should be very acceptable for interpretation at scales up to 1:50,000 and useful for change mapping probably up to scale 1:24,000. Striping visible in water bodies for both natural and color products indicates that the detector calibration is probably performing below preflight specification. For a set of 512 x 512 windows within the NE Arkansas scene, the variance-covariance matrices were computed and principal component analyses performed. Initial analysis suggests that the shortwave infrared TM 5 and 6 channels are a highly significant data source. The thermal channel (TM 7) shows negative correlation with TM 1 and 4.

Assessing forest damage in high-elevation coniferous forests in Vermont and New Hampshire using Thematic Mapper data

NASA Technical Reports Server (NTRS)

Vogelmann, James E.; Rock, Barrett N.

1988-01-01

This study evaluates the potential of measuring/mapping forest damage in spruce-fir forests in the Green Mountains of Vermont and White Mountains of New Hampshire using Landsat Thematic Mapper (TM) data. The TM 1.65/0.83-micron (TM5/4) and 2.22/0.83-micron (TM7/4) band ratios were found to correlate well with ground-based measurements of forest damage (a measure of percentage foliar loss) at 11 spruce-fir stands located on Camels Hump, a mountain in northern Vermont. Images using 0.56 and 1.65-micron bands with 1.65/0.83-micron band ratios indicated locations of heavy conifer forest damage. Both 1.65/0.83 and 2.22/0.83-micron band ratios were used to quantify levels of conifer forest damage among individual mountains throughout many of the Green and White Mountains. Damage was found to be consistently higher for the Green than the White Mountains.

Stabilization of the μ-opioid receptor by truncated single transmembrane splice variants through a chaperone-like action.

PubMed

Xu, Jin; Xu, Ming; Brown, Taylor; Rossi, Grace C; Hurd, Yasmin L; Inturrisi, Charles E; Pasternak, Gavril W; Pan, Ying-Xian

2013-07-19

The μ-opioid receptor gene, OPRM1, undergoes extensive alternative pre-mRNA splicing, as illustrated by the identification of an array of splice variants generated by both 5' and 3' alternative splicing. The current study reports the identification of another set of splice variants conserved across species that are generated through exon skipping or insertion that encodes proteins containing only a single transmembrane (TM) domain. Using a Tet-Off system, we demonstrated that the truncated single TM variants can dimerize with the full-length 7-TM μ-opioid receptor (MOR-1) in the endoplasmic reticulum, leading to increased expression of MOR-1 at the protein level by a chaperone-like function that minimizes endoplasmic reticulum-associated degradation. In vivo antisense studies suggested that the single TM variants play an important role in morphine analgesia, presumably through modulation of receptor expression levels. Our studies suggest the functional roles of truncated receptors in other G protein-coupled receptor families.

Comparison of MSS and TM Data for Landcover Classification in the Chesapeake Bay Area: a Preliminary Report. [Taylor's Island, Maryland

NASA Technical Reports Server (NTRS)

Mulligan, P. J.; Gervin, J. C.; Lu, Y. C.

1985-01-01

An area bordering the Eastern Shore of the Chesapeake Bay was selected for study and classified using unsupervised techniques applied to LANDSAT-2 MSS data and several band combinations of LANDSAT-4 TM data. The accuracies of these Level I land cover classifications were verified using the Taylor's Island USGS 7.5 minute topographic map which was photointerpreted, digitized and rasterized. The the Taylor's Island map, comparing the MSS and TM three band (2 3 4) classifications, the increased resolution of TM produced a small improvement in overall accuracy of 1% correct due primarily to a small improvement, and 1% and 3%, in areas such as water and woodland. This was expected as the MSS data typically produce high accuracies for categories which cover large contiguous areas. However, in the categories covering smaller areas within the map there was generally an improvement of at least 10%. Classification of the important residential category improved 12%, and wetlands were mapped with 11% greater accuracy.

Linkage studies on 13 biochemical loci and 2 coat color loci in a [(BN x TM) x TM] backcross progeny of the rat (Rattus norvegicus).

PubMed

Yamada, J; Hamada, S; Bender, K; Adams, M

1986-10-01

In a [(BN X TM) X TM] backcross progeny of rats, nine significant linkage associations were found among 105 pairwise combinations of 15 loci. After comparing this with other published data and data of personal communications, we considered that the d gene we tentatively designated may be identical to the gene for pink-eyed dilution (p), and that the associations of Gc-Hbb, RT1-h, and Gc-Fh were due to chance rather than real linkage. The linkages obtained in this study, therefore, were Hbb-p (26.5 +/- 5.5) in LG I, Mup-1-Acon-1 (12.5 +/- 4.1) in LG II, Hao-1-Svp-1 (23.8 +/- 6.6) in LG IV, Es-1-Es-3 (17.2 +/- 4.7) in LG V, h-Gc (10.9 +/- 3.3) in LG VI, and Fh-Pep-3 (32.3 +/- 5.9) in LG X.

Y-chromosomal variation in Sub-Saharan Africa: insights into the history of Niger-Congo groups

PubMed Central

de Filippo, Cesare; Barbieri, Chiara; Whitten, Mark; Mpoloka, Sununguko Wata; Gunnarsdóttir, Ellen Drofn; Bostoen, Koen; Nyambe, Terry; Beyer, Klaus; Schreiber, Henning; de Knijff, Peter; Luiselli, Donata; Stoneking, Mark; Pakendorf, Brigitte

2013-01-01

Technological and cultural innovations, as well as climate changes, are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ~10,000 years ago. The expansion of Bantu languages (a family within the Niger-Congo phylum) ~5,000 years ago represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sub-lineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, D.R.C, and Zambia). With the inclusion of published data, we analyzed 2736 individuals from 26 groups representing all linguistic phyla and covering a large portion of Sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using Linear Discriminant Analysis on STR haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggest that their expansion throughout Sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible. PMID:21109585

Pyrosequencing Reveals Soil Enzyme Activities and Bacterial Communities Impacted by Graphene and Its Oxides.

PubMed

Rong, Yan; Wang, Yi; Guan, Yina; Ma, Jiangtao; Cai, Zhiqiang; Yang, Guanghua; Zhao, Xiyue

2017-10-25

Graphene (GN) and graphene oxides (GOs) are novel carbon nanomaterial; they have been attracting much attention because of their excellent properties and are widely applied in many areas, including energy, electronics, biomedicine, environmental science, etc. With industrial production and consumption of GN/GO, they will inevitably enter the soil and water environments. GN/GO may directly cause certain harm to microorganisms and lead to ecological and environmental risks. GOs are GN derivatives with abundant oxygen-containing functional groups in their graphitic backbone. The structure and chemistry of GN show obvious differences compared to those of GO, which lead to the different environmental behaviors. In this study, four different types of soil (S1-S4) were employed to investigate the effect of GN and GO on soil enzymatic activity, microbial population, and bacterial community through pyrosequencing of 16S rRNA gene amplicons. The results showed that soil enzyme activity (invertase, protease, catalase, and urease) and microbial population (bacteria, actinomycetes, and fungi) changed after GN/GO release into soils. Soil microbial community species are more rich, and the diversity also increases after GO/GN application. The phylum of Proteobacteria increased at 90 days after treatment (DAT) after GN/GO application. The phylum of Chloroflexi occurred after GN application at 90 DAT in S1 soil and reached 4.6%. Proteobacteria was the most abundant phylum in S2, S3, and S4 soils; it ranged from 43.6 to 71.4% in S2 soil, from 45.6 to 73.7% in S3 soil, and from 38.1 to 56.7% in S4 soil. The most abundant genera were Bacillus (37.5-47.0%) and Lactococcus (28.0-39.0%) in S1 soil, Lysobacter and Flavobacterium in S2 soil, Pedobacter in S3 soil, and Massilia in S4 soil. The effect of GN and GO on the soil microbial community is time-dependent, and there are no significant differences between the samples at 10 and 90 DAT.

Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups.

PubMed

de Filippo, Cesare; Barbieri, Chiara; Whitten, Mark; Mpoloka, Sununguko Wata; Gunnarsdóttir, Ellen Drofn; Bostoen, Koen; Nyambe, Terry; Beyer, Klaus; Schreiber, Henning; de Knijff, Peter; Luiselli, Donata; Stoneking, Mark; Pakendorf, Brigitte

2011-03-01

Technological and cultural innovations as well as climate changes are thought to have influenced the diffusion of major language phyla in sub-Saharan Africa. The most widespread and the richest in diversity is the Niger-Congo phylum, thought to have originated in West Africa ∼ 10,000 years ago (ya). The expansion of Bantu languages (a family within the Niger-Congo phylum) ∼ 5,000 ya represents a major event in the past demography of the continent. Many previous studies on Y chromosomal variation in Africa associated the Bantu expansion with haplogroup E1b1a (and sometimes its sublineage E1b1a7). However, the distribution of these two lineages extends far beyond the area occupied nowadays by Bantu-speaking people, raising questions on the actual genetic structure behind this expansion. To address these issues, we directly genotyped 31 biallelic markers and 12 microsatellites on the Y chromosome in 1,195 individuals of African ancestry focusing on areas that were previously poorly characterized (Botswana, Burkina Faso, Democratic Republic of Congo, and Zambia). With the inclusion of published data, we analyzed 2,736 individuals from 26 groups representing all linguistic phyla and covering a large portion of sub-Saharan Africa. Within the Niger-Congo phylum, we ascertain for the first time differences in haplogroup composition between Bantu and non-Bantu groups via two markers (U174 and U175) on the background of haplogroup E1b1a (and E1b1a7), which were directly genotyped in our samples and for which genotypes were inferred from published data using linear discriminant analysis on short tandem repeat (STR) haplotypes. No reduction in STR diversity levels was found across the Bantu groups, suggesting the absence of serial founder effects. In addition, the homogeneity of haplogroup composition and pattern of haplotype sharing between Western and Eastern Bantu groups suggests that their expansion throughout sub-Saharan Africa reflects a rapid spread followed by backward and forward migrations. Overall, we found that linguistic affiliations played a notable role in shaping sub-Saharan African Y chromosomal diversity, although the impact of geography is clearly discernible.

Large enhancement of light extraction efficiency in AlGaN-based nanorod ultraviolet light-emitting diode structures.

PubMed

Ryu, Han-Youl

2014-02-04

Light extraction efficiency (LEE) of AlGaN-based nanorod deep ultraviolet (UV) light-emitting diodes (LEDs) is numerically investigated using three-dimensional finite-difference time-domain simulations. LEE of deep UV LEDs is limited by strong light absorption in the p-GaN contact layer and total internal reflection. The nanorod structure is found to be quite effective in increasing LEE of deep UV LEDs especially for the transverse magnetic (TM) mode. In the nanorod LED, strong dependence of LEE on structural parameters such as the diameter of a nanorod and the p-GaN thickness is observed, which can be attributed to the formation of resonant modes inside the nanorod structure. Simulation results show that, when the structural parameters of the nanorod LED are optimized, LEE can be higher than 50% and 60% for the transverse electric (TE) and TM modes, respectively. The nanorod structure is expected to be a good candidate for the application to future high-efficiency deep UV LEDs. PACS: 41.20.Jb; 42.72.Bj; 85.60.Jb.

Large enhancement of light extraction efficiency in AlGaN-based nanorod ultraviolet light-emitting diode structures

PubMed Central

2014-01-01

Light extraction efficiency (LEE) of AlGaN-based nanorod deep ultraviolet (UV) light-emitting diodes (LEDs) is numerically investigated using three-dimensional finite-difference time-domain simulations. LEE of deep UV LEDs is limited by strong light absorption in the p-GaN contact layer and total internal reflection. The nanorod structure is found to be quite effective in increasing LEE of deep UV LEDs especially for the transverse magnetic (TM) mode. In the nanorod LED, strong dependence of LEE on structural parameters such as the diameter of a nanorod and the p-GaN thickness is observed, which can be attributed to the formation of resonant modes inside the nanorod structure. Simulation results show that, when the structural parameters of the nanorod LED are optimized, LEE can be higher than 50% and 60% for the transverse electric (TE) and TM modes, respectively. The nanorod structure is expected to be a good candidate for the application to future high-efficiency deep UV LEDs. PACS 41.20.Jb; 42.72.Bj; 85.60.Jb PMID:24495598

Space Environmental Effects on the Optical Properties of Selected Transparent Polymers

NASA Technical Reports Server (NTRS)

Edwards, David L.; Willowby, Douglas J.; Hubbs, Whitney C.; Piszczor, Michael F., Jr.; Bowden, Mary L.

1997-01-01

Transparent polymer films are currently considered for use as solar concentrating lenses for spacecraft power and propulsion systems. These polymer films concentrate solar energy onto energy conversion devices such as solar cells and thermal energy systems. Conversion efficiency is directly related to the polymer transmission. Space environmental effects will decrease the transmission and thus reduce the conversion efficiency. This investigation focuses on the effects of ultraviolet and charged particle radiation on the transmission of selected transparent polymers. Multiple candidate polymer samples were exposed to near ultraviolet (NUV) radiation to screen the materials and select optimum materials for further study. All materials experienced transmission degradation of varying degree. A method was developed to normalize the transmission loss and thus rank the materials according to their tolerance of NUV. Teflon(Tm) FEP and Teflon(Tm) PFA were selected for further study. These materials were subjected to a combined charged particle dose equivalent to 5 years in a typical geosynchronous Earth orbit (GEO). Results from these NUV screening tests and the 5 year GEO equivalent dose are presented.

Secondary Forest Age and Tropical Forest Biomass Estimation Using TM

NASA Technical Reports Server (NTRS)

Nelson, R. F.; Kimes, D. S.; Salas, W. A.; Routhier, M.

1999-01-01

The age of secondary forests in the Amazon will become more critical with respect to the estimation of biomass and carbon budgets as tropical forest conversion continues. Multitemporal Thematic Mapper data were used to develop land cover histories for a 33,000 Square kM area near Ariquemes, Rondonia over a 7 year period from 1989-1995. The age of the secondary forest, a surrogate for the amount of biomass (or carbon) stored above-ground, was found to be unimportant in terms of biomass budget error rates in a forested TM scene which had undergone a 20% conversion to nonforest/agricultural cover types. In such a situation, the 80% of the scene still covered by primary forest accounted for over 98% of the scene biomass. The difference between secondary forest biomass estimates developed with and without age information were inconsequential relative to the estimate of biomass for the entire scene. However, in futuristic scenarios where all of the primary forest has been converted to agriculture and secondary forest (55% and 42% respectively), the ability to age secondary forest becomes critical. Depending on biomass accumulation rate assumptions, scene biomass budget errors on the order of -10% to +30% are likely if the age of the secondary forests are not taken into account. Single-date TM imagery cannot be used to accurately age secondary forests into single-year classes. A neural network utilizing TM band 2 and three TM spectral-texture measures (bands 3 and 5) predicted secondary forest age over a range of 0-7 years with an RMSE of 1.59 years and an R(Squared) (sub actual vs predicted) = 0.37. A proposal is made, based on a literature review, to use satellite imagery to identify general secondary forest age groups which, within group, exhibit relatively constant biomass accumulation rates.

Morphology evolution and pure red upconversion mechanism of β-NaLuF4 crystals.

PubMed

Lin, Hao; Xu, Dekang; Li, Anming; Teng, Dongdong; Yang, Shenghong; Zhang, Yueli

2016-06-16

A series of β-NaLuF4 crystals were synthesized via a hydrothermal method. Hexagonal phase microdisks, microprisms, and microtubes were achieved by simply changing the amount of citric acid in the initial reaction solution. Pure red upconversion (UC) luminescence can be observed in β-NaLuF4:Yb(3+), Tm(3+), Er(3+) and Li(+) doped β-NaLuF4:20% Yb(3+), 1% Tm(3+), 20% Er(3+). Based on the rate equations, we report the theoretical model about the pure red UC mechanism in Yb(3+)/Tm(3+)/Er(3+) doped system. It is proposed that the pure red UC luminescence is mainly ascribed to the energy transfer UC from Tm(3+):(3)F4 → (3)H6 to Er(3+):(4)I11/2 → (4)F9/2 and the cross-relaxation (CR) effect [Er(3+):(4)S3/2 + (4)I15/2 → (4)I9/2 + (4)I13/2] rather than the long-accepted mechanism [CR process among Er(3+):(4)F7/2 + (4)I11/2 → (4)F9/2 + (4)F9/2]. In addition, compared to the Li(+)-free counterpart, the pure red UC luminescence in β-NaLuF4:20% Yb(3+), 1% Tm(3+), 20% Er(3+) with 15 mol% Li(+) doping is enhanced by 13.7 times. This study provides a general and effective approach to obtain intense pure red UC luminescence, which can be applied to other synthetic strategies.

Morphology evolution and pure red upconversion mechanism of β-NaLuF4 crystals

PubMed Central

Lin, Hao; Xu, Dekang; Li, Anming; Teng, Dongdong; Yang, Shenghong; Zhang, Yueli

2016-01-01

A series of β-NaLuF4 crystals were synthesized via a hydrothermal method. Hexagonal phase microdisks, microprisms, and microtubes were achieved by simply changing the amount of citric acid in the initial reaction solution. Pure red upconversion (UC) luminescence can be observed in β-NaLuF4:Yb3+, Tm3+, Er3+ and Li+ doped β-NaLuF4:20% Yb3+, 1% Tm3+, 20% Er3+. Based on the rate equations, we report the theoretical model about the pure red UC mechanism in Yb3+/Tm3+/Er3+ doped system. It is proposed that the pure red UC luminescence is mainly ascribed to the energy transfer UC from Tm3+:3F4 → 3H6 to Er3+:4I11/2 → 4F9/2 and the cross-relaxation (CR) effect [Er3+:4S3/2 + 4I15/2 → 4I9/2 + 4I13/2] rather than the long-accepted mechanism [CR process among Er3+:4F7/2 + 4I11/2 → 4F9/2 + 4F9/2]. In addition, compared to the Li+-free counterpart, the pure red UC luminescence in β-NaLuF4:20% Yb3+, 1% Tm3+, 20% Er3+ with 15 mol% Li+ doping is enhanced by 13.7 times. This study provides a general and effective approach to obtain intense pure red UC luminescence, which can be applied to other synthetic strategies. PMID:27306720

Total Mucosal Irradiation with Intensity-modulated Radiotherapy in Patients with Head and Neck Carcinoma of Unknown Primary: A Pooled Analysis of Two Prospective Studies.

PubMed

Richards, T M; Bhide, S A; Miah, A B; Del Rosario, L; Bodla, S; Thway, K; Gujral, D M; Rooney, K P; Schick, U; McGovern, T; Grove, L; Newbold, K L; Harrington, K J; Nutting, C M

2016-09-01

To determine the clinical outcomes of an intensity-modulated radiotherapy technique for total mucosal irradiation (TM-IMRT) in patients with head and neck carcinoma of unknown primary (HNCUP). A single-centre prospective phase II trial design was used in two sequential studies to evaluate TM-IMRT for HNCUP. Patients were investigated for primary tumour site using examination under anaesthetic and biopsies, computed tomography ± magnetic resonance imaging (MRI) or 18-fluorodeoxyglucose positron emission tomography-computed tomography (PET-CT). Patients received IMRT to the potential primary tumour sites and elective cervical nodes. Concomitant chemotherapy was used in patients who received primary radiotherapy or those with nodal extracapsular extension. Thirty-six patients with HNCUP were recruited; 72% male. Twenty-five patients (69.4%) had p16-positive disease. Two year mucosal and local nodal control rates were 97.1% (95% confidence interval 91.4-100) and 89.8% (78.4-100), respectively. One mucosal primary was detected 7.3 months after TM-IMRT and three patients died from recurrent/metastatic squamous cell carcinoma of the head and neck. Twelve patients (33%) developed grade 3 (Late Effects in Normal Tissue-Subjective, Objective, Management and Analytical; LENT-SOMA) dysphagia with a 1 year enteric tube feeding rate of 2.7%. The high-grade subjective xerostomia rate (LENT-SOMA) at 24 months after IMRT was 15%. At a median follow-up of 36.1 months, the use of TM-IMRT was associated with good local control. Toxicity was comparable with previously reported TM-IMRT regimens encompassing similar mucosal volumes. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Performance of continuous wave and acousto-optically Q-switched Tm, Ho: YAP laser pumped by diode laser

NASA Astrophysics Data System (ADS)

Li, Guoxing; Xie, Wenqiang; Yang, Xining; Zhang, Ziqiu; Zhang, Hongda; Zhang, Liang

2018-02-01

A two-end-pumped a-cut Tm(0.5%), Ho(0.5%):YAP laser output at 2119nm is reported under cryogenic temperature. The maximum output power reached to 7.76W with the incident pump power of 24.2W in CW mode. With the acousto-optically Q-switch, an average power of 7.3W can be obtained, when the pulse repetition frequency was 7.5 kHz. The corresponding optical-to-optical conversion efficiency was 30.2% and the slope efficiency was 31.4%. Then, the laser output characteristics in the repetition frequency of 7.5 kHz and 10kHz were researched. The output power, the optical-to-optical conversion efficiency and slope efficiency were increased with the increase of the repetition frequency. In the same repetition frequency, the pulse duration was decreasing with the growth of the incident pump power.

Comparison of tunable lasers based on diode pumped Tm-doped crystals

NASA Astrophysics Data System (ADS)

Šulc, Jan; Jelínková, Helena; Koranda, Petr; Černý, Pavel; Jabczyński, Jan K.; Żendzian, Waldemar; Kwiatkowski, Jacek; Urata, Yoshiharu; Higuchi, Mikio

2008-12-01

We report on continuously tunable operation of a diode pumped lasers based on Tm-doped materials, emitting in the 1.8 - 2.μ1 m spectral band. In our study we compare results obtained with three various single crystals doped by Tm3+ ions: Yttrium Aluminum perovskite YAP (YAlO3), Gadolinium orthovanadate GdVO4, and Yttrium Lithium Fluoride YLF (YLiF4). Following samples were available: the 3mm long a-cut crystal rod of Tm:YAP with 4% at. Tm/Y (diameter 3 mm); the 8mm long b-cut crystal rod of Tm:YLF with 3.5% at. Tm/Y (diameter 3 mm); the 2.7mm long a-cut crystal block of Tm:GdVO4 with 2% at. Tm/Gd (crystal face 5×3 mm). For active medium pumping, the laser diode radiation was used. Because the tested samples differs significantly in absorption spectra, two fibre-coupled (core diameter 400 µm) temperature-tuned laser diodes were used: first operating at wavelength 793nm was used for Tm:YAP and Tm:YLF; the second operating at wavelength 802nm was used for Tm:GdVO4. In both cases, the continuous power up to 20W was available for pumping. The diode radiation was focused into the active crystal by two achromatic doublet lenses with the focal length f = 75 mm. The measured radius of pumping beam focus inside the crystal was 260 µm. The longitudinally diode pumped crystals were tested in linear, 80mm long, hemispherical laser cavity. The curved (radius 150mm) output coupler reflectivity was ~ 97 % in range from 1.8 up to 2.1 μm. The pumping flat mirror had maximal reflectivity in this range and it had high transmission around 0.8 μm. A 1.5mm thick birefringent plate made from quartz (Lyot filter) inserted under a Brewster's angle was used as a tuning element. This plate was placed inside the resonator between the crystal and the output coupler. Using Tm:YAP crystal, the maximal output power of 2.8W in this set-up was obtained. The laser could be tuned from 1865nm up to 2036nm with a maximum at 1985 nm. Laser based on Tm:YLF crystal was tunable from 1835nm up to 2010nm with a maximum at 1928 nm (3.0W was reached). Using the Tm:GdVO4 tunable operation with greater that 1W output at 1920nm and 130nm tuning range (1842-1972 nm) was demonstrated. The overall reached tuning range of over 200nm covers many important atmospheric absorption lines and contains also the local absorption peak of liquid water, making them attractive for applications such as high resolution spectroscopy, atmospheric remote sensing, laser radar, and laser microsurgery.

Genome Sequence of the Verrucomicrobium Opitutus terrae PB90-1, an Abundant Inhabitant of Rice Paddy Soil Ecosystems▿

PubMed Central

van Passel, Mark W. J.; Kant, Ravi; Palva, Airi; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Glavina del Rio, Tijana; Pitluck, Sam; Goltsman, Eugene; Clum, Alicia; Sun, Hui; Schmutz, Jeremy; Larimer, Frank W.; Land, Miriam L.; Hauser, Loren; Kyrpides, Nikolaos; Mikhailova, Natalia; Richardson, P. Paul; Janssen, Peter H.; de Vos, Willem M.; Smidt, Hauke

2011-01-01

Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice paddy soil and capable of propionate production from plant-derived polysaccharides. PMID:21398538

Twenty-Five Years of Landsat Thermal Band Calibration

NASA Technical Reports Server (NTRS)

Barsi, Julia A.; Markham, Brian L.; Schoff, John R.; Hook, Simon J.; Raqueno, Nina G.

2010-01-01

Landsat-7 Enhanced Thematic Mapper+ (ETM+), launched in April 1999, and Landsat-5 Thematic Mapper (TM), launched in 1984, both have a single thermal band. Both instruments thermal band calibrations have been updated previously: ETM+ in 2001 for a pre-launch calibration error and TM in 2007 for data acquired since the current era of vicarious calibration has been in place (1999). Vicarious calibration teams at Rochester Institute of Technology (RIT) and NASA/Jet Propulsion Laboratory (JPL) have been working to validate the instrument calibration since 1999. Recent developments in their techniques and sites have expanded the temperature and temporal range of the validation. The new data indicate that the calibration of both instruments had errors: the ETM+ calibration contained a gain error of 5.8% since launch; the TM calibration contained a gain error of 5% and an additional offset error between 1997 and 1999. Both instruments required adjustments in their thermal calibration coefficients in order to correct for the errors. The new coefficients were calculated and added to the Landsat operational processing system in early 2010. With the corrections, both instruments are calibrated to within +/-0.7K.

High-power graphene mode-locked Tm/Ho co-doped fiber laser with evanescent field interaction.

PubMed

Li, Xiaohui; Yu, Xuechao; Sun, Zhipei; Yan, Zhiyu; Sun, Biao; Cheng, Yuanbing; Yu, Xia; Zhang, Ying; Wang, Qi Jie

2015-11-16

Mid-infrared ultrafast fiber lasers are valuable for various applications, including chemical and biomedical sensing, material processing and military applications. Here, we report all-fiber high-power graphene mode-locked Tm/Ho co-doped fiber laser at long wavelength with evanescent field interaction. Ultrafast pulses up to 7.8 MHz are generated at a center wavelength of 1879.4 nm, with a pulse width of 4.7 ps. A graphene absorber integrated with a side-polished fiber can increase the damage threshold significantly. Harmonics mode-locking can be obtained till to the 21(th) harmonics at a pump power of above 500 mW. By using one stage amplifier in the anomalous dispersion regime, the laser can be amplified up to 450 mW and the narrowest pulse duration of 1.4 ps can be obtained simultaneously. Our work paves the way to graphene Tm/Ho co-doped mode-locked all-fiber master oscillator power amplifiers as potentially efficient and economic laser sources for high-power laser applications, such as special material processing and nonlinear optical studies.

Shear Bond Strength of DentStat(trademark) for Bracket Bonding to Gold, Ceramic, and Enamel

DTIC Science & Technology

2012-12-21

i Shear bond strength of DentStatTM for bracket bonding to gold, ceramic, and enamel . A THESIS Presented to the Faculty of Uniform...in the thesis manuscript entitled: ’Shear Bond Strength of DentStatTM for Bracket Bonding to Gold, Ceramic, and Enamel ’ is appropriately...Ceramic, and Enamel ’ 7. Intended publication/meeting: June 2013 8. "Required by" date: 1 July 2013 9. Date of submission for USU approval: 6 June

ONR/MARCORSYSCOM Evaluation of Self-Applied Tourniquets for Combat Applications

DTIC Science & Technology

2005-11-01

dicrotic notch in the IPG pulse, 5. Maximum amplitude of the postdicrotic segment of the IPG pulse, 6. Peak of the EKG QRS complex immediately after the...IPG pulse until the occurrence of the dicrotic notch (Wu, 1992). TOUT (s) Time of excess venous outflow = (tM7 - tM4), (Al 0) the time period from...the dicrotic notch until the end of the IPG pulse (Wu, 1992). Note that A, ST, and EXHT are measures of pulse morphology independent of heart rate. In

∼2 μm emission properties and non-radiative processes of Tm{sup 3+} in germanate glass

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

Gao, Song; Liu, Xueqiang; Fan, Xiaokang

2014-11-07

In this paper, 80GeO{sub 2}-8Ga{sub 2}O{sub 3}-10BaO-2Nb{sub 2}O{sub 5}-6PbO (in mol%) glass samples with different Tm{sub 2}O{sub 3} concentrations (0, 0.5, 0.75, 1, 1.25, and 1.5 mol. %) were prepared by traditional melt-quenching method. According to the measurement of thermal properties of the host glass, the glass transition temperature is 596.7 °C and no crystallization peak is observed. Judd–Ofelt parameters Ω{sub t} (t = 2, 4, 6) and fluorescent lifetimes were obtained by Judd-Ofelt theory. The similar values of Judd–Ofelt parameters and the full-width at half-maximums of ∼1800 nm indicate the local environment of Tm{sup 3+} changes little with increment of Tm{sub 2}O{sub 3} concentrations.more » Maximum stimulated emission cross-section of ∼1800 nm is 6.22 × 10{sup −21} cm{sup 2} as calculated by Fuchtbauer–Ladenburg formula. Energy migration among Tm{sup 3+} ions was analyzed by the extended overlap integral method. The non-radiative transition rates between mainly energy levels of Tm{sup 3+} were calculated. Non-radiative transition rate of {sup 3}F{sub 4} energy level caused by OH was analyzed by rate equation and deduced by fitting the fluorescence decay curve.« less

Comparative analysis of pentavalent rotavirus vaccine strains and G8 rotaviruses identified during vaccine trial in Africa.

PubMed

Heylen, Elisabeth; Zeller, Mark; Ciarlet, Max; Lawrence, Jody; Steele, Duncan; Van Ranst, Marc; Matthijnssens, Jelle

2015-10-06

RotaTeqTM is a pentavalent rotavirus vaccine based on a bovine rotavirus genetic backbone in vitro reassorted with human outer capsid genes. During clinical trials of RotaTeqTM in Sub-Saharan Africa, the vaccine efficacy over a 2-year follow-up was lower against the genotypes contained in the vaccine than against the heterotypic G8P[6] and G8P[1] rotavirus strains of which the former is highly prevalent in Africa. Complete genome analyses of 43 complete rotavirus genomes collected during phase III clinical trials of RotaTeqTM in Sub-Saharan Africa, were conducted to gain insight into the high level of cross-protection afforded by RotaTeqTM against these G8 strains. Phylogenetic analysis revealed the presence of a high number of bovine rotavirus gene segments in these human G8 strains. In addition, we performed an in depth analysis on the individual amino acid level which showed that G8 rotaviruses were more similar to the RotaTeqTM vaccine than non-G8 strains. Because RotaTeqTM possesses a bovine genetic backbone, the high vaccine efficacy against G8 strains might be partially explained by the fact that all these strains contain a complete or partial bovine-like backbone. Altogether, this study supports the hypothesis that gene segments other than VP7 and VP4 play a role in vaccine-induced immunity.

Thermal manipulations during broiler incubation alter performance of broilers to 70 days of age.

PubMed

Piestun, Y; Druyan, S; Brake, J; Yahav, S

2013-05-01

Recent decades have seen significant progress in the genetic selection of fast-growing broiler chickens. Whereas in many countries the average marketing age is 5 to 6 wk, the US, French, and other markets demand heavier broilers (~4 kg) that require a longer posthatching growing period. With greater age and greater BW, the ability to cope with hot weather conditions deteriorates, which can result in increased economic losses during periods of hot weather. Recent studies have demonstrated a long-lasting effect of intermittent thermal manipulation (TM) during embryogenesis, when it was applied for 12 h/d between embryonic (E) days E7 and E16, which was shown by improved thermotolerance during acute posthatching heat stress as well as improved feed conversion ratio (FCR) and breast muscle yield. The present study was designed to elucidate the effect of TM during embryogenesis on Cobb 500 broiler performance up to 70 d of age. Hatchability and male BW were not affected by TM, but TM females demonstrated a lower (P = 0.024) BW during the entire 70-d posthatching study. However, following embryonic TM, both sexes exhibited lower (P = 0.028 and P = 0.018 for males and females, respectively) feed intake and body temperature accompanied by improved FCR and greater breast muscle weight. In light of the present and previous studies, it was concluded that intermittent TM during broiler embryonic development had a long-lasting effect on energy balance that led to improved FCR and breast muscle yield.

Maturation of Rb+ and PAH accumulation by rabbit anterior uvea and choroid plexus

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

Krupin, T.; Fritz, C.; Becker, B.

In vitro accumulation of radioactive para-aminohippuric acid (/sup 3/H-PAH) and rubidium (/sup 86/Rb+) by the anterior uvea, ciliary processes, and the choroid plexus was evaluated in tissues from newborn and various aged rabbits. Accumulation of PAH was present in the anterior uvea at 1 day of age (tissue to media ratio, T/M, of 2.1 +/- 0.2) and remained at this level for the first 14 days of life. Accumulation did not rise to adult levels until 21 days of age (T/M 5.5 +/- 0.6). Rubidium accumulation in the anterior uvea, a measure of Na+, K+-pump activity, was higher than adultmore » values 6 hr after birth (T/M25.2 +/- 0.9). Activity remained elevated through day 28 and did not fall to adult levels until day 60 (T/M 13.4 +/- 0.6). Accumulation studies on isolated ciliary processes were similar to those obtained from anterior uveal tissue. Daily subcutaneous injections of penicillin (300,000 units/kg/day) for 1 week had no effect on anterior uvea PAH accumulation (penicillin T/M was 1.7 +/- 0.1 and saline control T/M was 2.0 +/- 0.2). Accumulation of either /sup 3/H-PAH or /sup 86/Rb+ by the choroid plexus was present 1 day after birth in amounts that were similar to adult values and did not change during the 90 days of testing.« less

Anatomy and relations of the infraspinatus and the teres minor muscles: a fresh cadaver dissection study.

PubMed

Bacle, Guillaume; Gregoire, Jean-Marc; Patat, Frédéric; Clavert, Philippe; de Pinieux, Gonzague; Laulan, Jacky; Lakhal, Walid; Favard, Luc

2017-02-01

Despite their functional importance, the infraspinatus (ISP) and teres minor (TM) muscles have been little investigated. This study aimed to describe the macroscopic morphology, innervation, and inter-relations of the ISP and TM muscles. Forty fresh cadaver dissections and histologic analysis were performed. Three groups of specimens were distinguished according to the rotator cuff tendon status: (1) intact rotator cuff; (2) supraspinatus tendon tears with intact ISP tendon; and (3) both supraspinatus and ISP tendons torn. Muscle fiber organization and muscle and tendon length were recorded. ISP and TM innervation and fiber structure were studied. ISP muscles were composed of three groups of fiber organized in two planes: two superficial groups, with mean pennation angles of, respectively, 27° ± 4° and 23° ± 3° with respect to the axis of the central tendon of the underlying group. TMs were thick fusiform muscles showing a parallel organization; 26 specimens (67 %) had aponeuroses isolating the TM, with a mean length of 5.2 ± 2.7 cm. Rotator cuff lesions were associated with relatively greater ISP tendon than muscle length. Innervation of the ISP muscle comprised 2-4 main branches from the suprascapular nerve and that of the TM 1 branch from the axillary nerve. ISP muscle body morphology derives from three groups of fibers in two planes. The TM has a parallel organization. Several nerve branches innervate the ISP muscle, whereas only one supplies the TM. The limits between the two muscles bodies consist of an aponeurotic fascia in two-thirds of cases.

Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes.

PubMed

Lyukmanova, E N; Shenkarev, Z O; Khabibullina, N F; Kopeina, G S; Shulepko, M A; Paramonov, A S; Mineev, K S; Tikhonov, R V; Shingarova, L N; Petrovskaya, L E; Dolgikh, D A; Arseniev, A S; Kirpichnikov, M P

2012-03-01

Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Acute Demyelinating Events Following Vaccines: A Case-Centered Analysis.

PubMed

Baxter, Roger; Lewis, Edwin; Goddard, Kristin; Fireman, Bruce; Bakshi, Nandini; DeStefano, Frank; Gee, Julianne; Tseng, Hung Fu; Naleway, Allison L; Klein, Nicola P

2016-12-01

 Case reports have suggested that vaccines may trigger transverse myelitis (TM) or acute disseminated encephalomyelitis (ADEM), but the evidence for a causal association is inconclusive. We analyzed the association of immunization and subsequent development of TM or ADEM.  We identified all cases of TM and ADEM in the Vaccine Safety Datalink population. Using a case-centered method, we compared vaccination of each case to vaccination of all matched persons in the study population, who received the same type of vaccine, with respect to whether or not their vaccination occurred during a predetermined exposure interval. We calculated a risk difference (excess risk) of TM and ADEM for each vaccine.  Following nearly 64 million vaccine doses, only 7 cases of TM and 8 cases of ADEM were vaccinated during the primary exposure window 5-28 days prior to onset. For TM, there was no statistically significant increased risk of immunization. For ADEM, there was no statistically significant increased risk following any vaccine except for Tdap (adolescent and adult tetanus, reduced diphtheria, acellular pertussis) vaccine. Based on 2 exposed cases, the odds ratio for Tdap exposure 5-28 days prior to ADEM onset was 15.8 (95% confidence interval [CI], 1.2-471.6; P = .04), and the estimated excess risk was 0.385 (95% CI, -.04 to 1.16) cases per million doses.  We found no association between TM and prior immunization. There was a possible association of ADEM with Tdap vaccine, but the excess risk is not likely to be more than 1.16 cases of ADEM per million vaccines administered. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

ER Stress Induced by Tunicamycin Triggers α-Synuclein Oligomerization, Dopaminergic Neurons Death and Locomotor Impairment: a New Model of Parkinson's Disease.

PubMed

Cóppola-Segovia, Valentín; Cavarsan, Clarissa; Maia, Flavia G; Ferraz, Anete C; Nakao, Lia S; Lima, Marcelo Ms; Zanata, Silvio M

2017-10-01

Parkinson's disease (PD) is a neurodegenerative disorder characterized by progressive death of dopaminergic neurons of the substantia nigra pars compacta (SNpc), leading to the major clinical abnormalities that characterize this disease. Although PD's etiology is unknown, α-synuclein aggregation plays a pivotal role in PD pathogenesis, which could be associated to some pathological processes such as oxidative stress, endoplasmic reticulum (ER) stress, impaired protein degradation, and mitochondrial dysfunction. Increasing experimental evidence indicates that ER stress is involved in PD, however most of the described results employed cultured cell lines and genetically modified animal models. In this study, we developed a new ER stress rat model employing the well-known ER stressor tunicamycin (Tm). To evaluate if ER stress was able to induce PD features, we performed an intranigral injection of Tm (0.1 μg/cerebral hemisphere) and animals (male Wistar rats) were analyzed 7 days post injection. The classical 6-OHDA neurotoxin model (1 μg/cerebral hemisphere) was used as an established positive control for PD. We show that Tm injection induced locomotor impairment, dopaminergic neurons death, and activation of astroglia. In addition, we observed an extensive α-synuclein oligomerization in SNpc of Tm-injected animals when compared with DMSO-injected controls. Finally, both Tm and 6-OHDA treated animals presented increased levels of ER stress markers. Taken together, these findings show for the first time that the ER stressor Tm recapitulates some of the phenotypic characteristics observed in rodent models of PD, reinforcing the concept that ER stress could be an important contributor to the pathophysiology of PD. Therefore, we propose the intranigral Tm injection as a new ER stress-based model for the study of PD in vivo.

Short-term survival of the trabecular metal cup is similar to that of standard cups used in acetabular revision surgery.

PubMed

Mohaddes, Maziar; Rolfson, Ola; Kärrholm, Johan

2015-02-01

The use of trabecular metal (TM) cups in revision surgery has increased worldwide during the last decade. Since the introduction of the TM cup in Sweden in 2006, this design has gradually replaced other uncemented designs used in Sweden. According to data from the Swedish Hip Arthroplasty Register (SHAR) in 2012, one-third of all uncemented first-time cup revisions were performed using a TM cup. We compared the risk of reoperation and re-revision for TM cups and the 2 other most frequently used cup designs in acetabular revisions reported to the SHAR. The hypothesis was that the performance of TM cups is as good as that of established designs in the short term. The study population consisted of 2,384 patients who underwent 2,460 revisions during the period 2006 through 2012. The most commonly used cup designs were the press-fit porous-coated cup (n = 870), the trabecular metal cup (n = 805), and the cemented all-polyethylene cup (n = 785). 54% of the patients were female, and the median age at index revision was 72 (19-95) years. Reoperation was defined as a second surgical intervention, and re-revision-meaning exchange or removal of the cup-was used as endpoint. The mean follow-up time was 3.3 (0-7) years. There were 215 reoperations, 132 of which were re-revisions. The unadjusted and adjusted risk of reoperation or re-revision was not significantly different for the TM cup and the other 2 cup designs. Our data support continued use of TM cups in acetabular revisions. Further follow-up is necessary to determine whether trabecular metal cups can reduce the re-revision rate in the long term, compared to the less costly porous press-fit and cemented designs.

An Expanded Genomic Representation of the Phylum Cyanobacteria

PubMed Central

Soo, Rochelle M.; Skennerton, Connor T.; Sekiguchi, Yuji; Imelfort, Michael; Paech, Samuel J.; Dennis, Paul G.; Steen, Jason A.; Parks, Donovan H.; Tyson, Gene W.; Hugenholtz, Philip

2014-01-01

Molecular surveys of aphotic habitats have indicated the presence of major uncultured lineages phylogenetically classified as members of the Cyanobacteria. One of these lineages has recently been proposed as a nonphotosynthetic sister phylum to the Cyanobacteria, the Melainabacteria, based on recovery of population genomes from human gut and groundwater samples. Here, we expand the phylogenomic representation of the Melainabacteria through sequencing of six diverse population genomes from gut and bioreactor samples supporting the inference that this lineage is nonphotosynthetic, but not the assertion that they are strictly fermentative. We propose that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives. Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum. PMID:24709563

Classification of Active Microwave and Passive Optical Data Based on Bayesian Theory and Mrf

NASA Astrophysics Data System (ADS)

Yu, F.; Li, H. T.; Han, Y. S.; Gu, H. Y.

2012-08-01

A classifier based on Bayesian theory and Markov random field (MRF) is presented to classify the active microwave and passive optical remote sensing data, which have demonstrated their respective advantages in inversion of surface soil moisture content. In the method, the VV, VH polarization of ASAR and all the 7 TM bands are taken as the input of the classifier to get the class labels of each pixel of the images. And the model is validated for the necessities of integration of TM and ASAR, it shows that, the total precision of classification in this paper is 89.4%. Comparing with the classification with single TM, the accuracy increase 11.5%, illustrating that synthesis of active and passive optical remote sensing data is efficient and potential in classification.

Growth and spectroscopic properties of Tm3+:NaBi(MoO4)2 single crystal

NASA Astrophysics Data System (ADS)

Gusakova, N. V.; Mudryi, A. V.; Demesh, M. P.; Yasukevich, A. S.; Pavlyuk, A. A.; Kornienko, A. A.; Dunina, E. B.; Khodasevich, I. A.; Orlovich, V. A.; Kuleshov, N. V.

2018-06-01

In this work we report the spectroscopic properties of Tm3+:NaBi(MoO4)2 crystals with the dopant concentrations of 0.7 at.% and 3 at.%. The energy levels of the Tm3+ in the NaBi(MoO4)2 host were determined from polarized optical absorption and photoluminescence spectra measured at 77.4 K. Radiative properties of the crystals were calculated in context of Judd-Ofelt theory. Raman spectra of the crystal were studied. The concentration dependences of emission decay times of 3H4 and 3F4 levels were analyzed. The potential of the crystal for building tunable and ultrafast pulse lasers is shown on the base of cross sections and gain coefficient in the range of 1.9 μm.

Growth and spectral-luminescent study of SrMoO4 crystals doped with Tm3+ ions

NASA Astrophysics Data System (ADS)

Dunaeva, E. E.; Zverev, P. G.; Doroshenko, M. E.; Nekhoroshikh, A. V.; Ivleva, L. I.; Osiko, V. V.

2016-03-01

SrMoO4 crystals doped with Tm3+ ions have been produced from a melt using the Czochralski method; their spectral-luminescent characteristics have been studied, and laser radiation has been generated at the wavelength of 1.94 μm using laser-diode excitation. The high absorption section at the wavelength of 795 nm, the fairly high luminescence section, the long lifetime at the upper laser level 3F4 of 1.5 ms, and a wide luminescence band allow one to hope for developing efficient tunable Tm3+: SrMoO4 crystal lasers with diode pumping in the range of 1.7-2.0 μm, which are capable of implementing SRS self-transformation of radiation into the middle IR band.

The role of the atrial electromechanical delay in predicting atrial fibrillation in beta-thalassemia major patients.

PubMed

Rago, Anna; Russo, Vincenzo; Papa, Andrea Antonio; Ciardiello, Carmine; Pannone, Bruno; Mayer, Maria Carolina; Cimmino, Giovanni; Nigro, Gerardo

2017-03-01

Paroxysmal atrial tachyarrhythmias frequently occur in beta-thalassemia major (β-TM) patients. The aim of the current study was to evaluate the atrial electromechanical delay (AEMD) in a large β-TM population with normal cardiac function and its relationship to atrial fibrillation (AF) onset. Eighty β-TM patients (44 men, 36 women), with a mean age of 36.2 ± 11.1 years, and 80 healthy subjects used as controls, matched for age and gender, were studied for the occurrence of AF during a 5-year follow-up, through 30-day external loop recorder (ELR) monitoring performed every 6 months. Intra-AEMD and inter-AEMD of both atria were measured through tissue Doppler echocardiography. P-wave dispersion (PD) was carefully measured using 12-lead electrocardiogram (ECG). Compared to the healthy control group, the β-TM patients showed a statistically significant increase in inter-AEMD, intra-left AEMD, maximum P-wave duration, and PD. Dividing the β-TM group into two subgroups (patients with or without AF), the inter-AEMD, intra-left AEMD, maximum P-wave duration, and PD were significantly higher in the subgroup with AF compared to the subgroup without AF. There were significant good correlations of intra-left AEMD and inter-AEMD with PD. A cut-off value of 40.1 ms for intra-left AEMD had a sensitivity of 76.2% and a specificity of 97.5% in identifying β-TM patients with AF risk. A cut-off value of 44.8 ms for inter-AEMD had a sensitivity of 81.2% and a specificity of 98.7% in identifying this category of patients. Our results showed that the echocardiographic atrial electromechanical delay indices (intra-left and inter-AEMD) and the PD were significantly increased in β-TM subjects with normal cardiac function. PD and AEMD represent non-invasive, inexpensive, useful, and simple parameters to assess the AF risk in β-TM patients.

Reliability and validity of the Chinese version of the Pediatric Quality Of Life InventoryTM (PedsQLTM) 3.0 neuromuscular module in children with Duchenne muscular dystrophy.

PubMed

Hu, Jun; Jiang, Li; Hong, Siqi; Cheng, Li; Kong, Min; Ye, Yuanzhen

2013-03-15

The Pediatric Quality of Life Inventory(TM) (PedsQL(TM)) is a widely used instrument to measure pediatric health-related quality of life (HRQOL) in children aged 2 to 18 years. The current study aimed to evaluate the reliability and validity of the Chinese version of the PedsQL(TM) 3.0 Neuromuscular Module in children with Duchenne muscular dystrophy (DMD). The PedsQL(TM) 3.0 Neuromuscular Module was translated into Chinese following PedsQL(TM) Measurement Model Translation Methodology. The Chinese version scale was administered to 56 children with DMD and their parents, and the psychometric properties were evaluated. The missing value percentages for each item of the Chinese version scale ranged from 0.00% to 0.54%. Internal consistency reliability approached or exceeded the minimum reliability standard of α = 0.7 (child α = 0.81, parent α = 0.86). Test-retest reliability was satisfactory, with intraclass correlation coefficients (ICCs) of 0.66 for children and 0.88 for parents (P < 0.01). Correlation coefficients between iteims and their hypothesized subscales were higher than those with other subscales (P < 0.05). The subscale of "About My/My Child's Neuromuscular Disease" significantly related to mobility and stair climbing status (Child t = 2.21, Parent t = 2.83, P < 0.05). The inter-correlations among the Chinese version of the PedsQL(TM) 3.0 Neuromuscular Module and the PedsQL(TM) 4.0 Generic Core Scales had medium to large effect sizes (P < 0.05). The child self-report scores were in moderate agreement with the parent proxy-report scores (ICC = 0.51, P < 0.05). The Chinese version of the PedsQLTM 3.0 Neuromuscular Module has acceptable psychometric properties. It is a reliable measure of disease-specific HRQOL in Chinese children with DMD.

Initiation of Levodopa-Carbidopa Intestinal Gel Infusion Using Telemedicine (Video Communication System) Facilitates Efficient and Well-Accepted Home Titration in Patients with Advanced Parkinson’s Disease

PubMed Central

Willows, Thomas; Dizdar, Nil; Nyholm, Dag; Widner, Håkan; Grenholm, Peter; Schmiauke, Ursula; Urbom, Anna; Groth, Kristina; Larsson, Jörgen; Permert, Johan; Kjellander, Susanna

2017-01-01

Background: Levodopa-carbidopa intestinal gel (LCIG; Duodopa®) is used for continuous infusion in advanced Parkinson’s disease. To achieve optimal effect, the LCIG dose is individually titrated, traditionally conducted during hospitalization in Sweden. However, dose adjustment depends on surrounding conditions, physical activity, and emotional stress, which is why titration at home could be beneficial. Telemedicine (TM) using a video communication system offers alternative titration procedures, allowing LCIG initiation at home. Objective: Study objectives were to show the feasibility of TM for LCIG home titration, evaluate resource use, and assess patient, neurologist, and nurse satisfaction. Methods: Four clinics enrolled 15 patients to observe efficiency and feasibility of TM-based monitoring. Results: Patient median (range) age was 67 (52–73) years and time since diagnosis was 10 (7–23) years. Median time between LCIG initiation and end of TM-assisted titration was 2.8 (2.0–13.8) days. Median time required for home titration by neurologists, nurses, and patients was (hours:minutes) 1 : 14 (0 : 29–1 : 52), 5 : 49 (2 : 46–10 : 3), and 8 : 53 (4 : 11–14 : 11), respectively. Neurologists and nurses considered this to be less time than required for hospital titration. TM allowed patients 92% free time from start to end of titration. Technical problems associated with TM contacts were rare, mostly related to digital link, and quickly resolved. Patients, neurologists, and nurses were satisfied using TM. No serious adverse events were reported; there was one device complaint (tube occlusion). Conclusions: In this study, TM-assisted LCIG titration at home was resource-efficient, technically feasible, well-accepted and was deemed satisfactory by patients, neurologists, and nurses. PMID:28984615

Concentration of the macrolide antibiotic tulathromycin in broncho-alveolar cells is influenced by comedication of rifampicin in foals.

PubMed

Venner, Monica; Peters, Jette; Höhensteiger, Nina; Schock, Birthe; Bornhorst, Alexa; Grube, Markus; Adam, Ulrike; Scheuch, Eberhard; Weitschies, Werner; Rosskopf, Dieter; Kroemer, Heyo K; Siegmund, Werner

2010-02-01

Macrolide antibiotics penetrate in the lung against steep concentration gradients into the epithelial lining fluid (ELF) and broncho-alveolar cells (BAC). Since they interact with ABCB1, ABCC2, and organic anion transporting proteins (OATPs), which are localized to lung tissue, pulmonary concentration may be influenced by rifampicin (RIF), an inducer and modulator of efflux and uptake transporters. We measured concentrations of tulathromycin (TM) in plasma, ELF and BAC in 21 warm-blooded foals 24 and 192 h after first and last intramuscular injection of 2.5 mg/kg TM once weekly for 6 weeks. In 11 foals, TM was combined with RIF (10 mg/kg twice daily), and mRNA expression of ABCB1 and ABCC2 in BAC was assessed before and after RIF. Affinity of TM to ABCB1 and ABCC2 was measured by transport assays using cell monolayers and membrane vesicles of MDCKII and 2008 cells transfected with ABCB1 and ABCC2, respectively. At steady state, TM concentrated manifold in ELF and BAC. Comedication of RIF significantly decreased the AUC of TM (18.5 +/- 4.0 versus 24.4 +/- 3.7 microg x h/ml, p < 0.05) and lowered its concentrations in plasma (24 h, 0.17 +/- 0.05 versus 0.24 +/- 0.05 microg/ml; 192 h, 0.05 +/- 0.01 versus 0.06 +/- 0.01 microg/ml) and BAC (24 h, 0.84 +/- 0.36 versus 1.56 +/- 1.02 microg/ml; 192 h, 0.60 +/- 0.23 versus 1.23 +/- 0.90 microg/ml, all p < 0.05). Treatment with rifampicin did not markedly induce ABCB1 and ABCC2 expression. TM had no affinity to ABCB1 and ABCC2 in vitro. Concentration of TM in the lung of foals was significantly lowered by comedication of rifampicin most likely caused by extrapulmonary mechanisms leading to lower plasma concentrations.

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

PubMed Central

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m. PMID:24205246

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

PubMed

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.

PubMed

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E; Geelhoed, Jeanine S; Strous, Marc; Ruff, S Emil

2017-12-01

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate- and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ' U Sabulitectum silens' and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate-reducing microbial communities and their adaptation to a dynamic environment. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors

PubMed Central

2016-01-01

Available crystal structures of opioid receptors provide a high-resolution picture of ligand binding at the primary (“orthosteric”) site, that is, the site targeted by endogenous ligands. Recently, positive allosteric modulators of opioid receptors have also been discovered, but their modes of binding and action remain unknown. Here, we use a metadynamics-based strategy to efficiently sample the binding process of a recently discovered positive allosteric modulator of the δ-opioid receptor, BMS-986187, in the presence of the orthosteric agonist SNC-80, and with the receptor embedded in an explicit lipid–water environment. The dynamics of BMS-986187 were enhanced by biasing the potential acting on the ligand–receptor distance and ligand–receptor interaction contacts. Representative lowest-energy structures from the reconstructed free-energy landscape revealed two alternative ligand binding poses at an allosteric site delineated by transmembrane (TM) helices TM1, TM2, and TM7, with some participation of TM6. Mutations of amino acid residues at these proposed allosteric sites were found to either affect the binding of BMS-986187 or its ability to modulate the affinity and/or efficacy of SNC-80. Taken together, these combined experimental and computational studies provide the first atomic-level insight into the modulation of opioid receptor binding and signaling by allosteric modulators. PMID:26841170

Performance evaluation and geologic utility of LANDSAT-4 thematic mapper data

NASA Technical Reports Server (NTRS)

Paylor, E. D.; Abrams, M. J.; Conel, J. E.; Kahle, A. B.; Lang, H. R.

1985-01-01

The overall objective of the project was to evaluate LANDSAT-4 Thematic Mapper (TM) data in the context of geologic applications. This involved a quantitative assessment of the data quality including the spatial and spectral characteristics realized by the instrument. Three test sites were selected for the study: (1) Silver Bell, Arizona; (2) Death Valley, California; and (3) Wind River/Bighorn Basin area, Wyoming. Conclusions include: (1) Artificial and natural targets can be used to atmospherically calibrate TM data and investigate scanner radiometry, atmospheric parameters, and construction of atmospheric Modulation Transfer Functions (MTF's), (2) No significant radiometric degradation occurs in TM data as a result of SCROUNGE processing; however, the data exhibit narrow digital number (DN) distributiosn suggesting that the configuration of the instrument is not optimal for each science applications, (30 Increased spatial resolution, 1:24,000 enlargement capability, and good geometric fidelity of TM data allow accurate photogeologic/geomorphic mapping, including relative age dating of alluvial fans, measurement of structural and bedding attitudes, and construction of such things as structural cross sections and stratigraphic columns. (4) TM bands 5 and 7 are particularly useful for geologic applications because they span a region of the spectrum not previously sampled by multispectral scanner data and are important for characterizing clay and carbonate materials.

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

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

Yang, Mingye; Wang, Lu, E-mail: lwang22@suda.edu.cn, E-mail: yyli@suda.edu.cn; Li, Min

2015-06-15

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N,more » the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.« less

Molecular switches of the κ opioid receptor triggered by 6′-GNTI and 5′-GNTI

PubMed Central

Cheng, Jianxin; Sun, Xianqiang; Li, Weihua; Liu, Guixia; Tu, Yaoquan; Tang, Yun

2016-01-01

The κ opioid receptor (κOR) is a member of G-protein-coupled receptors, and is considered as a promising drug target for treating neurological diseases. κOR selective 6′-GNTI was proved to be a G-protein biased agonist, whereas 5′-GNTI acts as an antagonist. To investigate the molecular mechanism of how these two ligands induce different behaviors of the receptor, we built two systems containing the 5′-GNTI-κOR complex and the 6′-GNTI-κOR complex, respectively, and performed molecular dynamics simulations of the two systems. We observe that transmembrane (TM) helix 6 of the κOR rotates about 4.6o on average in the κOR-6′-GNTI complex. Detailed analyses of the simulation results indicate that E2976.58 and I2946.55 play crucial roles in the rotation of TM6. In the simulation of the κOR-5′-GNTI system, it is revealed that 5′-GNTI can stabilize TM6 in the inactive state form. In addition, the kink of TM7 is stabilized by a hydrogen bond between S3247.47 and the residue V691.42 on TM1. PMID:26742690

Near-IR, blue, and UV generation by frequency conversion of a Tm:YAP laser

NASA Astrophysics Data System (ADS)

Cole, Brian; Goldberg, Lew; Chinn, Steve

2018-02-01

We describe generation of near-infrared (944nm, 970nm), blue (472nm, 485nm), and UV (236 nm) light by frequency up-conversion of 2 μm output of a compact and efficient passively Q-switched Tm:YAP laser. The Tm:YAP laser source was near diffraction limited with maximum Q-switched pulse peak power of 190 kW. For second harmonic generation (SHG) of NIR, both periodically poled lithium niobate (PPLN) and lithium tri-borate (LBO) were evaluated, with 58% conversion efficiency and 3.1 W of 970 nm power achieved with PPLN. The PPLN 970nm emission was frequency doubled in 20mm long type I LBO, generating 1.1 W at 485nm with a conversion efficiency of 34%. With LBO used for frequency doubling of 2.3 W of 1888 nm Tm:YAP output to 944nm, 860mW was generated, with 37% conversion efficiency. Using a second LBO crystal to generate the 4th harmonic, 545mW of 472nm power was generated, corresponding to 64% conversion efficiency. To generate the 8th harmonic of Tm:YAP laser emission, the 472nm output of the second LBO was frequency doubled in a 7mm long BBO crystal, generating 110 mW at 236nm, corresponding to 21% conversion efficiency.

Strain and order-parameter coupling in Ni-Mn-Ga Heusler alloys from resonant ultrasound spectroscopy

NASA Astrophysics Data System (ADS)

Salazar Mejía, C.; Born, N.-O.; Schiemer, J. A.; Felser, C.; Carpenter, M. A.; Nicklas, M.

2018-03-01

Resonant ultrasound spectroscopy and magnetic susceptibility experiments have been used to characterize strain coupling phenomena associated with structural and magnetic properties of the shape-memory Heusler alloy series Ni50 +xMn25 -xGa25 (x =0 , 2.5, 5.0, and 7.5). All samples exhibit a martensitic transformation at temperature TM and ferromagnetic ordering at temperature TC, while the pure end member (x =0 ) also has a premartensitic transition at TP M, giving four different scenarios: TC>TP M>TM,TC>TM without premartensitic transition, TC≈TM , and TC

Using Scribe to Select Fonts on the Penguin.

DTIC Science & Technology

1984-02-01

indicates several things about that font. The first segment of the name (for example, Helvetica or TimesRoman) may indicate its shape and form. The number...nesting mi0me Penguins wre classified in the phylum Chordat &. subohylum Vefletwa. ciMs Ayes, order Spheniciformee. family Sphenclae. *4xtiracted fromt...somtimes great distances--each fall to their nesting sites. Penguins are classified In thes phylum Chordate , subphylum Vertebrate, class Ave$, order

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Treesearch

C.L. Schoch; G.-H. Sung; F. Lopez-Giraldez

2009-01-01

We present a six-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the fungi are resolved for...

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans

PubMed Central

Dumesic, Phillip A.; Rosenblad, Magnus A.; Samuelsson, Tore; Nguyen, Tiffany; Moresco, James J.; Yates, John R.; Madhani, Hiten D.

2015-01-01

Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features—SRP RNA helix 8 and Srp54—in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development. PMID:26275773

Layered Crystal Structure, Color-Tunable Photoluminescence, and Excellent Thermal Stability of MgIn2P4O14 Phosphate-Based Phosphors.

PubMed

Zhang, Jing; Cai, Ge-Mei; Yang, Lv-Wei; Ma, Zhi-Yuan; Jin, Zhan-Peng

2017-11-06

Single-component white phosphors stand a good chance to serve in the next-generation high-power white light-emitting diodes. Because of low thermal stability and containing lanthanide ions with reduced valence state, most of reported phosphors usually suffer unstable color of lighting for practical packaging and comparably complex synthetic processes. In this work, we present a type of novel color-tunable blue-white-yellow-emitting MgIn 2 P 4 O 14 :Tm 3+ /Dy 3+ phosphor with high thermal stability, which can be easily fabricated in air. Under UV excitation, the MgIn 2 P 4 O 14 :Tm 0.02 Dy 0.03 white phosphor exhibits negligible thermal-quenching behavior, with a 99.5% intensity retention at 150 °C, relative to its initial value at room temperature. The phosphor host MgIn 2 P 4 O 14 was synthesized and reported for the first time. MgIn 2 P 4 O 14 crystallizes in the space group of C2/c (No. 15) with a novel layered structure built of alternate anionic and cationic layers. Its disordering structure, with Mg and In atoms co-occupying the same site, is believed to facilitate the energy transfer between rare-earth ions and benefit by sustaining the luminescence with increasing temperature. The measured absolute quantum yields of MgIn 2 P 4 O 14 :Dy 0.04 , MgIn 2 P 4 O 14 :Tm 0.01 Dy 0.04 , and MgIn 2 P 4 O 14 :Tm 0.02 Dy 0.03 phosphors under the excitation of 351 nm ultraviolet radiation are 70.50%, 53.24%, and 52.31%, respectively. Present work indicates that the novel layered MgIn 2 P 4 O 14 is a promising candidate as a single-component white phosphor host with an excellent thermal stability for near-UV-excited white-light-emitting diodes (wLEDs).

Forty-Year Calibrated Record of Earth-Surface Reflected Radiance from Landsat: A Review

NASA Technical Reports Server (NTRS)

Markham, Brian; Helder, Dennis

2011-01-01

Sensors on Landsat satellites have been collecting images of the Earth's surface for nearly 40 years. These images have been invaluable for characterizing and detecting changes in the land cover and land use of the world. Although initially conceived as primarily picture generating sensors, even the early sensors were radiometrically calibrated and spectrally characterized prior to launch and incorporated some capabilities to monitor their radiometric calibration once on orbit. Recently, as the focus of studies has shifted to monitoring Earth surface parameters over significant periods of time, serious attention has been focused toward bringing the data from all these sensors onto a common radiometric scale over this 40-year period. This effort started with the most recent systems and then was extended back in time. Landsat-7 ETM+, the best-characterized sensor of the series prior to launch and once on orbit, and the most stable system to date, was chosen to serve as the reference. The Landsat-7 project was the first of the series to build an image assessment system into its ground system, allowing systematic characterization of its sensors and data. Second, the Landsat-5 TM (still operating at the time of the Landsat-7 launch and continues to operate) calibration history was reconstructed based on its internal calibrator, vicarious calibrations, pseudo-invariant sites and a tie to Landsat-7 ETM+ at the time of the commissioning of Landsat-7. This process was performed in two iterations: the earlier one relied primarily on the TM internal calibrator. When this was found to have some deficiencies, a revised calibration was based more on pseudo-invariant sites, though the internal calibrator was still used to establish the short-term variations in response due to icing build up on the cold focal plane. As time progressed, a capability to monitor the Landsat-5 TM was added to the image assessment system. The Landsat-4 TM, which operated from 1982-1992, was the third system to which the radiometric scale was extended. The limited and broken use of the Landsat-4 TM made this analysis more difficult. Eight-day separated image pairs from Landsat-5 combined with analysis of pseudo invariant sites established this history. The fourth and most challenging effort was making the Landsat-1 to -5 MSS sensors' data internally radiometrically consistent. This effort was particularly complicated by the age of the MSS data, varying formats and processing levels in the archive, limited datasets, and limited documentation available. Ultimately, pseudo-invariant sites were identified in North America and used for this effort. Note that most of the Landsat-MSS archived data had already been calibrated using the MSS internal calibrators, so this processing was imbedded in the result. The final effort was developing an absolute scale for Landsat MSS similar to what was already established for the "TM" sensors. This was accomplished by using simultaneous data from Landsat-5 MSS and Landsat-5 TM, accounting for spectral differences between the sensors using EO-1 Hyperion data. The recalibrated history of the Landsat data and implications to users are discussed. The key result from this work is a consistently calibrated Landsat data archive that spans nearly 40 years with total uncertainties on the order of 10% or less for most sensors and bands.