A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

PubMed Central

Wlodarska, Marta; Johnston, James C.; Gardy, Jennifer L.

2015-01-01

SUMMARY Tuberculosis (TB) is an ancient disease with an enormous global impact. Despite declining global incidence, the diagnosis, phenotyping, and epidemiological investigation of TB require significant clinical microbiology laboratory resources. Current methods for the detection and characterization of Mycobacterium tuberculosis consist of a series of laboratory tests varying in speed and performance, each of which yields incremental information about the disease. Since the sequencing of the first M. tuberculosis genome in 1998, genomic tools have aided in the diagnosis, treatment, and control of TB. Here we summarize genomics-based methods that are positioned to be introduced in the modern clinical TB laboratory, and we highlight how recent advances in genomics will improve the detection of antibiotic resistance-conferring mutations and the understanding of M. tuberculosis transmission dynamics and epidemiology. We imagine the future TB clinic as one that relies heavily on genomic interrogation of the M. tuberculosis isolate, allowing for more rapid diagnosis of TB and real-time monitoring of outbreak emergence. PMID:25810419

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

Structural and magnetic properties of morphotropic phase boundary involved Tb 1-xGd xFe 2 compounds

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

Murtaza, Adil; Yang, Sen; Zhou, Chao

2016-09-01

In the present paper, structural, magnetic and magnetostrictive properties of Tb 1-xGd xFe 2 (0 <= x <= 1.0) were studied. Synchrotron x-ray diffraction (XRD) results show the non-cubic symmetry of Tb 1-xGd xFe 2 at room temperature and composition-induced crystallographic phase transition from rhombohedral phase to tetragonal phase. The Gd concentration dependent lattice parameters, lattice distortion and change of easy magnetic direction were detected by synchrotron XRD. With the Gd concentration increases, Curie temperature Tc increases while room temperature magnetization and magnetostriction coefficient lambda(111) and the anisotropy of TbFe 2 decrease. The decrease in spontaneous magnetostriction coefficient lambda(111) withmore » increasing Gd substitution can be understood on the basis of the single-ion model; the corresponding decrease of magnetostriction for Tb 1-xGd xFe 2, and the large magnetostriction value occurs on the Tb-rich side, are ascribed to decrease of lambda(111)« less

Structural, magnetic, magneto-caloric and Mössbauer spectral study of Tb{sub 2}Fe{sub 17} compound synthesized by arc melting

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

Charfeddine, S.; LVMU, Centre National de Recherches en Sciences des Matériaux, Technopole de Borj-Cédria, BP 73 Soliman 8027; Zehani, K.

We have synthesized the intermetallic Tb{sub 2}Fe{sub 17} compound in hexagonal crystal structure by arc-melting without annealing. X-ray diffraction pattern has been refined by Rietveld method. The crystal structure is hexagonal with P6{sub 3}/mmc space group (Th{sub 2}Ni{sub 17}-type). The Mössbauer spectrum of Tb{sub 2}Fe{sub 17} compound has been analyzed with seven magnetic sextets assigned to the inequivalent crystallographic sites. The temperature dependence of magnetization data revealed that Tb{sub 2}Fe{sub 17} exhibits a second-order ferromagnetic to paramagnetic phase transition in the vicinity of Curie temperature (T{sub C}=412 K). The relative cooling power around the magnetic transition and the Arrott plotsmore » are also reported. - Graphical abstract: A 3D surface showing the temperature and applied magnetic field dependencies of the magnetization for Tb{sub 2}Fe{sub 17} compound (left). Rietveld analysis of the XRD pattern (right). Crystal structure for the hexagonal P6{sub 3}/mmc Tb{sub 2}Fe{sub 17} (bottom). Display Omitted - Highlights: • Tb{sub 2}Fe{sub 17} single-phase synthesized by simple arc-melting without any heat treatment. • The crystal structure is hexagonal with P6{sub 3}/mmc space group. • The magnetic entropy change of the sample was determined by Maxwell relation. • Hyperfine parameters, magnetic and magnetocaloric properties were studied.« less

Treatment: Latent TB Infection (LTBI) and TB Disease

MedlinePlus

... Search Form Controls Cancel Submit Search The CDC Tuberculosis (TB) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Tuberculosis Basic TB Facts How TB Spreads Latent TB ...

Multi-quasiparticle excitations in145Tb

NASA Astrophysics Data System (ADS)

Zheng, Yong; Zhou, Xiaohong; Zhang, Yuhu; Liu, Minliang; Guo, Yingxiang; Lei, Xiangguo; Hayakawa, T.; Oshima, M.; Toh, T.; Shizuma, T.; Katakura, J.; Hatsukawa, Y.; Matsuda, M.; Kusakari, H.; Sugawara, M.

2004-09-01

High-spin states in145Tb have been populated using the118Sn (32S, 1p4n) reaction at beam energy of 165 MeV. The level scheme of145Tb has been established up to Ex≈7.4 MeV. The level scheme shows characteristics of a spherical or slightly oblate nucleus. Based on the systematic trends of the level structure in the neighboring N=80 isotones, the level structure in145Tb below 2 MeV excitation is well eplained by coupling an h 11/2 valence proton to the even-even144Gd core. Above 2 MeV excitation, most of the yrast levels are interpreted with multi-quasiparticle shell-model configurations.

Structure and luminescent property of complexes of aryl carboxylic acid-functionalized polystyrene with Eu(III) and Tb(III) ions.

PubMed

Gao, Baojiao; Shi, Nan; Qiao, Zongwen

2015-11-05

Via polymer reactions, naphthoic acid (NA) and benzoic acid (BA) were bonded onto the side chains of polystyrene (PS), respectively, and two aryl carboxylic acid-functionalized polystyrenes, PSNA and PSBA, were obtained. Using PSNA and PSBA as macromolecule ligands and Eu(3+) and Tb(3+) ions as central ions, various luminescent binary polymer-rare earth complexes were prepared. At the same time, with 1,10-phenanthroline (Phen) and 4,4'-bipyridine (Bipy) as small-molecule co-ligands, various ternary polymer-rare earth complexes were also prepared. On the basis of characterizing PSNA, PSBA and complexes, the relationship between structure and luminescent property for these prepared complexes were mainly investigated. The study results show that the macromolecule ligands PSNA and PSBA, or the bonded NA and BA ligands, can strongly sensitize the fluorescence emissions of Eu(3+) ion or Tb(3+) ion, but the sensitization effect is strongly dependent on the structure of the ligands and the property of the central ions, namely it is strongly dependent on the matching degree of energy levels. The fluorescence emission of the binary complex PS-(NA)3-Eu(III) is stronger than that PS-(BA)3-Eu(III), indicating ligand NA has stronger sensitization action for Eu(3+) ion than ligand BA; the binary complex PS-(BA)3-Tb(III) emit strong characteristic fluorescence of Tb(3+) ion, displaying that ligand BA can strongly sensitize Tb(3+) ion, whereas the binary complex PS-(NA)3-Tb(III) nearly does not emit the characteristic fluorescence of Tb(3+) ion, showing that ligand NA does not sensitize Tb(3+) ion. The fluorescence intensity of the ternary complexes is much stronger than that of the binary complexes in the same series. Copyright © 2015 Elsevier B.V. All rights reserved.

TB Terms

MedlinePlus

... Search Form Controls Cancel Submit Search The CDC Tuberculosis (TB) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Tuberculosis Basic TB Facts How TB Spreads Latent TB ...

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Synthesis, crystal structure, optical and thermal properties of lanthanide hydrogen-polyphosphates Ln[H(PO3)4] (Ln = Tb, Dy, Ho).

PubMed

Förg, Katharina; Höppe, Henning A

2015-11-28

Lanthanide hydrogen-polyphosphates Ln[H(PO3)4] (Ln = Tb, Dy, Ho) were synthesised as colourless (Ln = Tb, Dy) and light pink (Ln = Ho) crystalline powders by reaction of Tb4O7/Dy2O3/Ho2O3 with H3PO3 at 380 °C. All compounds crystallise isotypically (P2(1)/c (no. 14), Z = 4, a(Tb) = 1368.24(4) pm, b(Tb) = 710.42(2) pm, c(Tb) = 965.79(3) pm, β(Tb) = 101.200(1)°, 3112 data, 160 parameters, wR2 = 0.062, a(Ho) = 1363.34(5) pm, b(Ho) = 709.24(3) pm, c(Ho) = 959.07(4) pm, β(Ho) = 101.055(1)°, 1607 data, 158 parameters, wR2 = 0.058). The crystal structure comprises two different infinite helical chains of corner-sharing phosphate tetrahedra. In-between these chains the lanthanide ions are located, coordinated by seven oxygen atoms belonging to four different polyphosphate chains. Vibrational, UV/Vis and fluorescence spectra of Ln[H(PO3)4] (Ln = Tb, Dy, Ho) as well as Dy[H(PO3)4]:Ln (Ln = Ce, Eu) and the magnetic and thermal behaviour of Tb[H(PO3)4] are reported.

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

PubMed

Butler, J B; Vaillancourt, R E; Potts, B M; Lee, D J; King, G J; Baten, A; Shepherd, M; Freeman, J S

2017-05-22

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Tuning of magnetic ordering by Y substitution onto Tb site in the nanocrystalline TbMnO{sub 3}

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

Chakraborty, Keka R., E-mail: kekarc@barc.gov.in, E-mail: smyusuf@barc.gov.in; Mukadam, M. D.; Yusuf, S. M., E-mail: kekarc@barc.gov.in, E-mail: smyusuf@barc.gov.in

2015-10-28

We report the magnetic properties, of nano-crystalline powders Tb{sub 1−x}Y{sub x}MnO{sub 3} (x = 0, 0.1, 0.2, 0.3 and 0.4), as perceived by neutron diffraction, and elucidate the effect of Tb site substitution on the magnetic structure of TbMnO{sub 3}. All samples crystallized in the orthorhombic structure conforming to space group Pnma, and exhibited an incommensurate collinear antiferromagnetic ordering of the Mn ions below ∼40 K. Furthermore, at T ≤ 20 K, all these samples showed a change in magnetic structure (of Mn moments) to a spiral ordering down to 2 K, the lowest measured temperature. For the samples with x = 0, 0.1, and 0.2, a short-ranged twomore » dimensional (2D) ordering of Tb moments was also observed at 2 K. However, for the other samples (x = 0.3 and 0.4), no magnetic ordering of Tb moments was found down to 2 K. So with Y substitution, a crossover from 2D ordering to a disordering of Tb moments was observed. The moments at the Mn site were found to be lower than the full Mn{sup 3+} (4μ{sub B}) moment for all the samples below 40 K. The magnetic properties of all the samples studied by us in nano form are more pronounced than those of the reported single crystals of same compositions [V. Yu. Ivanov et al., JETP Lett. 91, 392–397 (2010)].« less

Deposition-temperature dependence of structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Elam, W. T.; Koon, N. C.; Hellman, F.

1994-02-01

The anisotropic local structure in a series of amorphous Tb26Fe74 films deposited at different deposition temperatures and having different magnetic anisotropy energies have been investigated using polarization-dependent extended x-ray-absorption fine-structure measurements. Samples deposited at temperatures >=300 K exhibit anisotropic pair correlations where like atomic pairs are favored in plane and unlike pairs are favored out of plane. Both the anisotropic pair correlations and the perpendicular magnetic anisotropy increase with increasing deposition temperature. In contrast, a sample deposited at 77 K was found to have isotropic pair correlations, low perpendicular magnetic anisotropy, and a large (~=1%) in-plane compression.

Screening contacts of patients with extrapulmonary TB for latent TB infection.

PubMed

Humphreys, Anna; Abbara, Aula; Williams, Sion; John, Laurence; Corrah, Tumena; McGregor, Alastair; Davidson, Robert N

2018-03-01

2016 TB National Institute for Health and Care Excellence (NICE) guidelines imply that contacts of extrapulmonary TB do not require screening for latent TB infection. At our high TB prevalence site, we identified 189 active cases of TB for whom there were 698 close contacts. 29.1% of the contacts of pulmonary TB and 10.7% of the contacts of extrapulmonary TB had active or latent TB infection. This supports screening contacts of extrapulmonary TB at our site and presents a way to access high-risk individuals. We propose to continue to screen the contacts of our patients with extrapulmonary TB and recommend other TB units audit their local results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Molecularly imprinted sensor based on Russian Matryoshka structured molecules for enhanced specific identification and double amplification in ultra-trace Tb3+ determination.

PubMed

Li, Jianping; Yang, Bin; Pan, Hongcheng; Xu, Guobao

2018-06-30

The selective and sensitive detection of rare earth elements is thought to be difficult because the concentration of those elements in the sample is commonly at a low level and they normally have severe mutual interference which is caused by homologous chemical properties. In this study, a novel molecularly imprinted polymer (MIP) sensor was fabricated for highly sensitive and selective determination of ultra-trace Tb 3+ . The Tb 3+ -ethylenediaminetetraacetic acid complex (Tb-EDTA) as the template molecule was incorporated into mono-6-mercapto-β-cyclodextrin (mono-6-SH-β-CD) to form a Russian Matryoshka (RM)-structured molecule (CD/Tb-EDTA). Titanium isopropoxide was utilized in vapor sol-gel polymerization to construct MIP membrane. Moreover, the selectivity of the RM MIP sensor was remarkably enhanced by the "triple-selectivity" recognition of EDTA-to-Tb 3+ , β-CD-to-(Tb-EDTA), and 3D cavity-to-(CD/Tb-EDTA), while the sensitivity of the MIP sensor was significantly improved by ECL signal enhancement based on double amplification, in other words, the electrochemiluminescence resonance energy transfer (ECL-RET) between the ECL donor of CD/Tb-EDTA and the ECL acceptor of Ru(bpy) 3 2+ , and the ECL enhancement by the co-reactant of CD/Tb-EDTA on Ru(bpy) 3 Cl 2 . When the imprinted cavities were occupied by Tb-EDTA during rebinding, the host-guest inclusion structured complex was formed and the ECL intensities produced by the Ru(bpy) 3 Cl 2 ECL system increased with increasing concentration of Tb-EDTA. The proposed sensor was used for quantitative analysis of Tb 3+ with concentrations ranging from 8.00 × 10 -13 mol/L to 4.00 × 10 -9 mol/L and successfully applied to detect Tb 3+ in seawater samples. The detection limit of the sensor was found to be 3.90 × 10 -13 mol/L (DL = 3δ b /K), which is lower than previously reported values. Thus, the fabricated sensor is feasible for practical applications. Copyright © 2018 Elsevier B.V. All rights

Phase equilibria in the Tb-Mg-Co system at 500 °C, crystal structure and hydrogenation properties of selected compounds

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

Shtender, V.V.; Denys, R.V.; Zavaliy, I.Yu., E-mail: zavaliy@ipm.lviv.ua

2015-12-15

The isothermal section of the Tb–Mg–Co phase diagram at 500 °C has been built on the basis of XRD analysis of forty samples prepared by powder metallurgy. The existence of two ternary compounds Tb{sub 4}Mg{sub 3}Co{sub 2} and Tb{sub 4}MgCo was confirmed. The formation of two solid solutions, Tb{sub 1−x}Mg{sub x}Co{sub 3} (0≤x≤0.4) and Tb{sub 1-−x}Mg{sub x}Co{sub 2} (0≤x≤0.6), was found for the first time. It is shown that Tb{sub 5}Mg{sub 24} also dissolves a small amount of Co. Other binary compounds do not dissolve the third component. The Tb{sub 4}MgCo and TbMgCo{sub 4} compounds form hydrides (12.7 and 5.3more » at.H/f.u. capacity, respectively) that retain the original structure of metallic matrices. Upon thermal desorption the Tb{sub 4}MgCoH{sub 12.7} hydride was stable up to 300 °C and disproportionated at higher temperature. Two other hydrides, Tb{sub 4}Mg{sub 3}Co{sub 2}H{sub ∼4} and Tb{sub 2}MgCo{sub 9}H{sub 12}, are unstable in air and decompose into the initial compounds. - Highlights: • The phase equilibria at 500 °°C in the Tb–Mg–Co system has been studied. • The existence of two ternary compounds, Tb{sub 4}Mg{sub 3}Co{sub 2} and Tb{sub 4}MgCo, was confirmed. • The formation of two solid solutions, Tb{sub 1−x}Mg{sub x}Co{sub 3} and Tb{sub 1−x}Mg{sub x}Co{sub 2}, was found. • Hydrogen sorption–desorption properties have been studied for the selected alloys.« less

TB control programmes: the challenges for Africa.

PubMed

Harries, T

1996-11-01

Governmental neglect of tuberculosis (TB), inadequately managed and inaccurately designed TB control programs, population growth, and the HIV epidemic account for the resurgence of TB in sub-Saharan Africa. The World Health Organization and the International Union against TB and Lung Disease have developed a TB control strategy that aims to reduce mortality, morbidity, and transmission of TB. It aims for an 85% cure rate among detected new cases of smear-positive TB and a 70% rate of detecting existing smear-positive TB cases. The strategy involves the provision of short-course chemotherapy (SCC) to all identified smear-positive TB cases through directly observed treatment (DOTS). SCC treatment regimens for smear-positive pulmonary TB recommended for sub-Saharan African countries are: initial phase = daily administration over 2 months of streptomycin, rifampicin, isoniazid, and pyrazinamide; continuation phase = 3 doses over 4 months of isoniazid and rifampicin or daily administration of thiacetazone and isoniazid or of ethambutol and isoniazid. A TB control policy must be implemented to bring about effective TB control. The essential elements of this policy include political commitment, case detection through passive case-finding, SCC, a regular supply of essential drugs, and a monitoring and evaluation system. Political commitment involves establishing a National TB Control Program to be integrated into the existing health structure. Increased awareness of TB in the community and among health workers and a reference laboratory are needed to make case finding successful. A distribution and logistics system is needed to ensure uninterrupted intake of drugs throughout treatment. These regimens have been very successful and cost-effective but pose several disadvantages (e.g., heavy workload of recommended 3 sputum smear tests). A simplified approach involves 1 initial sputum smear for 6 months; 6-months, intermittent rifampicin-based therapy, 100% DOTS throughout

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle.

PubMed

Raphaka, Kethusegile; Matika, Oswald; Sánchez-Molano, Enrique; Mrode, Raphael; Coffey, Mike Peter; Riggio, Valentina; Glass, Elizabeth Janet; Woolliams, John Arthur; Bishop, Stephen Christopher; Banos, Georgios

2017-03-23

The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics. The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control. The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB. Genomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle

TIME Impact - a new user-friendly tuberculosis (TB) model to inform TB policy decisions.

PubMed

Houben, R M G J; Lalli, M; Sumner, T; Hamilton, M; Pedrazzoli, D; Bonsu, F; Hippner, P; Pillay, Y; Kimerling, M; Ahmedov, S; Pretorius, C; White, R G

2016-03-24

Tuberculosis (TB) is the leading cause of death from infectious disease worldwide, predominantly affecting low- and middle-income countries (LMICs), where resources are limited. As such, countries need to be able to choose the most efficient interventions for their respective setting. Mathematical models can be valuable tools to inform rational policy decisions and improve resource allocation, but are often unavailable or inaccessible for LMICs, particularly in TB. We developed TIME Impact, a user-friendly TB model that enables local capacity building and strengthens country-specific policy discussions to inform support funding applications at the (sub-)national level (e.g. Ministry of Finance) or to international donors (e.g. the Global Fund to Fight AIDS, Tuberculosis and Malaria).TIME Impact is an epidemiological transmission model nested in TIME, a set of TB modelling tools available for free download within the widely-used Spectrum software. The TIME Impact model reflects key aspects of the natural history of TB, with additional structure for HIV/ART, drug resistance, treatment history and age. TIME Impact enables national TB programmes (NTPs) and other TB policymakers to better understand their own TB epidemic, plan their response, apply for funding and evaluate the implementation of the response.The explicit aim of TIME Impact's user-friendly interface is to enable training of local and international TB experts towards independent use. During application of TIME Impact, close involvement of the NTPs and other local partners also builds critical understanding of the modelling methods, assumptions and limitations inherent to modelling. This is essential to generate broad country-level ownership of the modelling data inputs and results. In turn, it stimulates discussions and a review of the current evidence and assumptions, strengthening the decision-making process in general.TIME Impact has been effectively applied in a variety of settings. In South Africa, it

Informational laws of genome structures

PubMed Central

Bonnici, Vincenzo; Manca, Vincenzo

2016-01-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

Informational laws of genome structures

NASA Astrophysics Data System (ADS)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

Interfacial exchange coupling and magnetization reversal in perpendicular [Co/Ni]N/TbCo composite structures.

PubMed

Tang, M H; Zhang, Zongzhi; Tian, S Y; Wang, J; Ma, B; Jin, Q Y

2015-06-15

Interfacial exchange coupling and magnetization reversal characteristics in the perpendicular heterostructures consisting of an amorphous ferrimagnetic (FI) TbxCo(100-x) alloy layer exchange-coupled with a ferromagnetic (FM) [Co/Ni]N multilayer have been investigated. As compared with pure TbxCo(100-x) alloy, the magnetization compensation composition of the heterostructures shift to a higher Tb content, implying Co/Ni also serves to compensate the Tb moment in TbCo layer. The net magnetization switching field Hc⊥ and interlayer interfacial coupling field Hex, are not only sensitive to the magnetization and thickness of the switched TbxCo(100-x) or [Co/Ni]N layer, but also to the perpendicular magnetic anisotropy strength of the pinning layer. By tuning the layer structure we achieve simultaneously both large Hc⊥ = 1.31 T and Hex = 2.19 T. These results, in addition to the fundamental interest, are important to understanding of the interfacial coupling interaction in the FM/FI heterostructures, which could offer the guiding of potential applications in heat-assisted magnetic recording or all-optical switching recording technique.

Enhancement of TbIII–CuII Single‐Molecule Magnet Performance through Structural Modification

PubMed Central

Heras Ojea, María José; Milway, Victoria A.; Velmurugan, Gunasekaran; Thomas, Lynne H.; Coles, Simon J.; Wilson, Claire; Wernsdorfer, Wolfgang

2016-01-01

Abstract We report a series of 3d–4f complexes {Ln2Cu3(H3L)2Xn} (X=OAc−, Ln=Gd, Tb or X=NO3 −, Ln=Gd, Tb, Dy, Ho, Er) using the 2,2′‐(propane‐1,3‐diyldiimino)bis[2‐(hydroxylmethyl)propane‐1,3‐diol] (H6L) pro‐ligand. All complexes, except that in which Ln=Gd, show slow magnetic relaxation in zero applied dc field. A remarkable improvement of the energy barrier to reorientation of the magnetisation in the {Tb2Cu3(H3L)2Xn} complexes is seen by changing the auxiliary ligands (X=OAc− for NO3 −). This leads to the largest reported relaxation barrier in zero applied dc field for a Tb/Cu‐based single‐molecule magnet. Ab initio CASSCF calculations performed on mononuclear TbIII models are employed to understand the increase in energy barrier and the calculations suggest that the difference stems from a change in the TbIII coordination environment (C 4v versus Cs). PMID:27484259

Magnetic properties and structural transitions of fluorite-related rare earth osmates Ln3OsO7 (Ln=Pr, Tb)

NASA Astrophysics Data System (ADS)

Hinatsu, Yukio; Doi, Yoshihiro

2013-02-01

Ternary rare-earth osmates Ln3OsO7 (Ln=Pr, Tb) have been prepared. They crystallize in an ortho-rhombic superstructure of cubic fluorite with space group Cmcm. Both of these compounds undergo a structural phase transition at 130 K (Ln=Pr) and 580 K (Ln=Tb). These compounds show complex magnetic behavior at low temperatures. Pr3OsO7 exhibits magnetic transitions at 8 and 73 K, and Tb3OsO7 magnetically orders at 8 and 60 K. The Os moments become one-dimensionally ordered, and when the temperature is furthermore decreased, it provokes the ordering in the Ln3+ sublattice that simultaneously becomes three-dimensionally ordered with the Os sublattice.

The association between ARV and TB drug resistance on TB treatment outcome among Kazakh TB/HIV patients.

PubMed

Mishkin, Kathryn; Alaei, Kamiar; Alikeyeva, Elmira; Paynter, Christopher; Aringazina, Altyn; Alaei, Arash

2018-02-26

TB drug resistance poses a serious threat to the public health of Kazakhstan. This paper presents findings related to TB treatment outcome and drug resistant status among people coinfected with HIV and TB in Kazakhstan. Cohort study using data were provided by the Kazakhstan Ministry of Health's National Tuberculosis Program for 2014 and 2015. Chi-square and logistical regression were performed to understand factors associated with drug resistant TB status and TB treatment outcome. In bivariate analysis, drug resistant status was significantly associated with year of TB diagnosis (p=0.001) viral load (p=0.03). TB treatment outcome was significantly associated with age at diagnosis (p=01), ARV treatment (p <0.0001), and TB drug resistant status (p=0.02). In adjusted analysis, drug resistance was associated with increased odds of successful completion of treatment with successful result compared to treatment failure (OR 6.94, 95% CI: 1.39-34.44) CONCLUSIONS: Our results suggest that being drug resistant is associated with higher odds of completing treatment with successful outcome, even when controlling for receipt of ARV therapy. Copyright © 2018. Published by Elsevier Ltd.

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Protein family clustering for structural genomics.

PubMed

Yan, Yongpan; Moult, John

2005-10-28

A major goal of structural genomics is the provision of a structural template for a large fraction of protein domains. The magnitude of this task depends on the number and nature of protein sequence families. With a large number of bacterial genomes now fully sequenced, it is possible to obtain improved estimates of the number and diversity of families in that kingdom. We have used an automated clustering procedure to group all sequences in a set of genomes into protein families. Bench-marking shows the clustering method is sensitive at detecting remote family members, and has a low level of false positives. This comprehensive protein family set has been used to address the following questions. (1) What is the structure coverage for currently known families? (2) How will the number of known apparent families grow as more genomes are sequenced? (3) What is a practical strategy for maximizing structure coverage in future? Our study indicates that approximately 20% of known families with three or more members currently have a representative structure. The study indicates also that the number of apparent protein families will be considerably larger than previously thought: We estimate that, by the criteria of this work, there will be about 250,000 protein families when 1000 microbial genomes have been sequenced. However, the vast majority of these families will be small, and it will be possible to obtain structural templates for 70-80% of protein domains with an achievable number of representative structures, by systematically sampling the larger families.

Effect of Tb{sup 3+} concentration on the optical and vibrational properties of YBO{sub 3} tri-doped with Eu{sup 3+}, Ce{sup 3+}, and Tb{sup 3+}

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

Sohal, S.; Hassanzadeh, E.; Huang, J. Y.

2014-05-14

Structural and optical studies are reported of yttrium orthoborate YBO{sub 3} when tri-doped with Eu{sup 3+}, Ce{sup 3+}, and Tb{sup 3+}, focusing on the role of terbium concentration. Incorporation of Tb{sup 3+} affects emission properties for photoluminescence (PL) excited by near ultraviolet light. For constant cerium and europium concentrations, increasing the Tb{sup 3+} results in diminished PL from the Ce{sup 3+} and Tb{sup 3+} color centers. Simultaneously, the PL excitation bands related to both Ce{sup 3+} and Tb{sup 3+} increase in intensity for red emission from the Eu{sup 3+}. Results are consistent with a Ce{sup 3+} → (Tb{sup 3+}){sub n} → Eu{sup 3+} energymore » transfer scheme, where (Tb{sup 3+}){sub n} denotes a chain incorporating n terbium ions. A high red to orange PL intensity ratio is obtained, ranging from 1.34 to 2.09. Raman vibrational bands show a systematic change, with Tb{sup 3+} concentration, in the B{sub 3}O{sub 9} ring terminal oxygen bending mode coordinated with the yttrium site where dopant ions substitute. The structural changes are interpreted as variations in the local neighborhood of these sites in the YBO{sub 3}:Ce{sup 3+},Tb{sup 3+},Eu{sup 3+} crystal structure.« less

Framework of behavioral indicators for outcome evaluation of TB health promotion: a Delphi study of TB suspects and Tb patients.

PubMed

Li, Ying; Ehiri, John; Hu, Daiyu; Zhang, Yanqi; Wang, Qingya; Zhang, Shun; Cao, Jia

2014-05-16

Health promotion for prevention and control of Tuberculosis (TB) is implemented worldwide because of its importance, but few reports have evaluated its impact on behavior due to a lack of standard outcome indicators. The objective of this study was to establish a framework of behavioral indicators for outcome evaluation of TB health promotion among TB suspects and patients. A two-round modified Delphi method involving sixteen TB control experts was used to establish a framework of behavioral indicators for outcome evaluation of TB health promotion targeted at TB suspects and patients. Sixteen of seventeen invited experts in TB control (authority score of 0.91 on a 1.0 scale) participated in round 1 survey. All sixteen experts also participated in a second round survey. After two rounds of surveys and several iterations among the experts, there was consensus on a framework of indicators for measuring outcomes of TB health promotion for TB suspects and patients. For TB suspects, the experts reached consensus on 2 domains ("Healthcare seeking behavior" and "Transmission prevention"), 3 subdomains ("Seeking care after onset of TB symptoms", "Pathways of seeking care" and "Interpersonal contact etiquette"), and 8 indicators (including among others, "Length of patient delay"). For TB patients, consensus was reached on 3 domains ("Adherence to treatment", "Healthy lifestyle" and "Transmission prevention"), 8 subdomains (including among others, "Adherence to their medication"), and 14 indicators (including "Percentage of patients who adhered to their medication"). Operational definitions and data sources were provided for each indicator. The findings of this study provide the basis for debate among international experts on a framework for achieving global consensus on outcome indicators for TB health promotion interventions targeted at TB patients and suspects. Such consensus will help to increase effectiveness of TB health promotion, while ensuring international

The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis.

PubMed

Rosenthal, Alex; Gabrielian, Andrei; Engle, Eric; Hurt, Darrell E; Alexandru, Sofia; Crudu, Valeriu; Sergueev, Eugene; Kirichenko, Valery; Lapitskii, Vladzimir; Snezhko, Eduard; Kovalev, Vassili; Astrovko, Andrei; Skrahina, Alena; Taaffe, Jessica; Harris, Michael; Long, Alyssa; Wollenberg, Kurt; Akhundova, Irada; Ismayilova, Sharafat; Skrahin, Aliaksandr; Mammadbayov, Elcan; Gadirova, Hagigat; Abuzarov, Rafik; Seyfaddinova, Mehriban; Avaliani, Zaza; Strambu, Irina; Zaharia, Dragos; Muntean, Alexandru; Ghita, Eugenia; Bogdan, Miron; Mindru, Roxana; Spinu, Victor; Sora, Alexandra; Ene, Catalina; Vashakidze, Sergo; Shubladze, Natalia; Nanava, Ucha; Tuzikov, Alexander; Tartakovsky, Michael

2017-11-01

The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/.

The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis

PubMed Central

Gabrielian, Andrei; Engle, Eric; Hurt, Darrell E.; Alexandru, Sofia; Crudu, Valeriu; Sergueev, Eugene; Kirichenko, Valery; Lapitskii, Vladzimir; Snezhko, Eduard; Kovalev, Vassili; Astrovko, Andrei; Skrahina, Alena; Harris, Michael; Long, Alyssa; Wollenberg, Kurt; Akhundova, Irada; Ismayilova, Sharafat; Skrahin, Aliaksandr; Mammadbayov, Elcan; Gadirova, Hagigat; Abuzarov, Rafik; Seyfaddinova, Mehriban; Avaliani, Zaza; Strambu, Irina; Zaharia, Dragos; Muntean, Alexandru; Ghita, Eugenia; Bogdan, Miron; Mindru, Roxana; Spinu, Victor; Sora, Alexandra; Ene, Catalina; Vashakidze, Sergo; Shubladze, Natalia; Nanava, Ucha; Tuzikov, Alexander; Tartakovsky, Michael

2017-01-01

ABSTRACT The TB Portals program is an international consortium of physicians, radiologists, and microbiologists from countries with a heavy burden of drug-resistant tuberculosis working with data scientists and information technology professionals. Together, we have built the TB Portals, a repository of socioeconomic/geographic, clinical, laboratory, radiological, and genomic data from patient cases of drug-resistant tuberculosis backed by shareable, physical samples. Currently, there are 1,299 total cases from five country sites (Azerbaijan, Belarus, Moldova, Georgia, and Romania), 976 (75.1%) of which are multidrug or extensively drug resistant and 38.2%, 51.9%, and 36.3% of which contain X-ray, computed tomography (CT) scan, and genomic data, respectively. The top Mycobacterium tuberculosis lineages represented among collected samples are Beijing, T1, and H3, and single nucleotide polymorphisms (SNPs) that confer resistance to isoniazid, rifampin, ofloxacin, and moxifloxacin occur the most frequently. These data and samples have promoted drug discovery efforts and research into genomics and quantitative image analysis to improve diagnostics while also serving as a valuable resource for researchers and clinical providers. The TB Portals database and associated projects are continually growing, and we invite new partners and collaborations to our initiative. The TB Portals data and their associated analytical and statistical tools are freely available at https://tbportals.niaid.nih.gov/. PMID:28904183

Magnetostructural phase transitions and magnetocaloric effect in Tb-Dy-Ho-Co-Al alloys with a Laves phase structure

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

Tereshina, I. S., E-mail: irina-tereshina@mail.ru; Baikov Institute of Metallurgy and Material Sciences, Russian Academy of Sciences, Moscow 119991; International Laboratory of High Magnetic Fields and Low Temperatures, Wroclaw 53-421

2016-07-07

The influence of simultaneous substitution within the rare earth (R) and Co sublattices on the structural, magnetic, and magnetocaloric properties of the Laves phase RCo{sub 2}-type compounds is studied. Main attention is devoted to the studies of the magnetostructural phase transitions and the transition types with respect to the alloy composition. Multicomponent alloys Tb{sub x}(Dy{sub 0.5}Ho{sub 0.5}){sub 1−x}Co{sub 2} and Tb{sub x}(Dy{sub 0.5}Ho{sub 0.5}){sub 1−x}Co{sub 1.75}Al{sub 0.25} were prepared with the use of high purity metals. Majority of the Tb{sub x}(Dy{sub 0.5}Ho{sub 0.5}){sub 1−x}Co{sub 2} alloys exhibit magnetic transitions of the first-order type and a large magnetocaloric effect. The substitutionmore » of Al for Co in Tb{sub x}(Dy{sub 0.5}Ho{sub 0.5}){sub 1−x}Co{sub 2} increases the Curie temperature (T{sub C}) but changes the transition type from first-to the second-order. The discussion of the physical mechanisms behind the observed phenomena is given on the basis of the first principles electronic-structure calculations taking into account both the atomic disorder and the magnetic disorder effects at finite temperatures. The advantage of Al-containing materials is that sufficiently high magnetocaloric effect values are preserved at T > T{sub C}.« less

Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome

PubMed Central

Li, Jian; Harris, R. Alan; Cheung, Sau Wai; Coarfa, Cristian; Jeong, Mira; Goodell, Margaret A.; White, Lisa D.; Patel, Ankita; Kang, Sung-Hae; Shaw, Chad; Chinault, A. Craig; Gambin, Tomasz; Gambin, Anna; Lupski, James R.; Milosavljevic, Aleksandar

2012-01-01

The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR–mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease. PMID:22615578

Multi-quasiparticle excitations in 145Tb

NASA Astrophysics Data System (ADS)

Zheng, Y.; Zhou, X. H.; Zhang, Y. H.; Hayakawa, T.; Oshima, M.; Toh, Y.; Shizuma, T.; Katakura, J.; Hatsukawa, Y.; Matsuda, M.; Kusakari, H.; Sugawara, M.; Furuno, K.; Komatsubara, T.

2004-04-01

High-spin states in 145Tb have been investigated by means of in-beam ggr-ray spectroscopy techniques with the 118Sn(32S, 1p4n) reaction. Excitation functions, X-ggr-t and ggr-ggr-t coincidences and ggr-ray anisotropies were measured. A level scheme of 145Tb was established up to Exap 7 MeV. The level structure shows characteristics of a spherical nucleus. Based on the systematics of level structure in the odd-A N = 80 isotones, the level structure below 2 MeV excitation is interpreted by coupling an h11/2 proton to the excitations in the even-even 144Gd core. Above 2 MeV excitation, most of the yrast levels are interpreted with multi-quasiparticle shell-model configurations.

Whole genome analysis of an MDR Beijing/W strain of Mycobacterium tuberculosis with large genomic deletions associated with resistance to isoniazid.

PubMed

Zhang, Qiufen; Wan, Baoshan; Zhou, Aiping; Ni, Jinjing; Xu, Zhihong; Li, Shuxian; Tao, Jing; Yao, YuFeng

2016-05-15

Mycobacterium tuberculosis (M.tb) is one of the most prevalent bacterial pathogens in the world. With geographical wide spread and hypervirulence, Beijing/W family is the most successful M.tb lineage. China is a country of high tuberculosis (TB) and high multiple drug-resistant TB (MDR-TB) burden, and the Beijing/W family strains take the largest share of MDR strains. To study the genetic basis of Beijing/W family strains' virulence and drug resistance, we performed the whole genome sequencing of M.tb strain W146, a clinical Beijing/W genotype MDR isolated from Wuxi, Jiangsu province, China. Compared with genome sequence of M.tb strain H37Rv, we found that strain W146 lacks three large fragments and the missing of furA-katG operon confers isoniazid resistance. Besides the missing of furA-katG operon, strain W146 harbored almost all known drug resistance-associated mutations. Comparison analysis of single nucleotide polymorphisms (SNPs) and indels between strain W146 and Beijing/W genotype strains and non-Beijing/W genotype strains revealed that strain W146 possessed some unique mutations, which may be related to drug resistance, transmission and pathogenicity. These findings will help to understand the large sequence polymorphisms (LSPs) and the transmission and drug resistance related genetic characteristics of the Beijing/W genotype of M.tb. Copyright © 2016 Elsevier B.V. All rights reserved.

Framework of behavioral indicators for outcome evaluation of TB health promotion: a Delphi study of TB suspects and Tb patients

PubMed Central

2014-01-01

Background Health promotion for prevention and control of Tuberculosis (TB) is implemented worldwide because of its importance, but few reports have evaluated its impact on behavior due to a lack of standard outcome indicators. The objective of this study was to establish a framework of behavioral indicators for outcome evaluation of TB health promotion among TB suspects and patients. Methods A two-round modified Delphi method involving sixteen TB control experts was used to establish a framework of behavioral indicators for outcome evaluation of TB health promotion targeted at TB suspects and patients. Results Sixteen of seventeen invited experts in TB control (authority score of 0.91 on a 1.0 scale) participated in round 1 survey. All sixteen experts also participated in a second round survey. After two rounds of surveys and several iterations among the experts, there was consensus on a framework of indicators for measuring outcomes of TB health promotion for TB suspects and patients. For TB suspects, the experts reached consensus on 2 domains (“Healthcare seeking behavior” and “Transmission prevention”), 3 subdomains (“Seeking care after onset of TB symptoms”, “Pathways of seeking care” and “Interpersonal contact etiquette”), and 8 indicators (including among others, “Length of patient delay”). For TB patients, consensus was reached on 3 domains (“Adherence to treatment”, “Healthy lifestyle” and “Transmission prevention”), 8 subdomains (including among others, “Adherence to their medication”), and 14 indicators (including “Percentage of patients who adhered to their medication”). Operational definitions and data sources were provided for each indicator. Conclusions The findings of this study provide the basis for debate among international experts on a framework for achieving global consensus on outcome indicators for TB health promotion interventions targeted at TB patients and suspects. Such consensus will help to

Risk Factors for Bovine Tuberculosis (bTB) in Cattle in Ethiopia.

PubMed

Dejene, Sintayehu W; Heitkönig, Ignas M A; Prins, Herbert H T; Lemma, Fitsum A; Mekonnen, Daniel A; Alemu, Zelalem E; Kelkay, Tessema Z; de Boer, Willem F

2016-01-01

Bovine tuberculosis (bTB) infection is generally correlated with individual cattle's age, sex, body condition, and with husbandry practices such as herd composition, cattle movement, herd size, production system and proximity to wildlife-including bTB maintenance hosts. We tested the correlation between those factors and the prevalence of bTB, which is endemic in Ethiopia's highland cattle, in the Afar Region and Awash National Park between November 2013 and April 2015. A total of 2550 cattle from 102 herds were tested for bTB presence using the comparative intradermal tuberculin test (CITT). Data on herd structure, herd movement, management and production system, livestock transfer, and contact with wildlife were collected using semi-structured interviews with cattle herders and herd owners. The individual overall prevalence of cattle bTB was 5.5%, with a herd prevalence of 46%. Generalized Linear Mixed Models with a random herd-effect were used to analyse risk factors of cattle reactors within each herd. The older the age of the cattle and the lower the body condition the higher the chance of a positive bTB test result, but sex, lactation status and reproductive status were not correlated with bTB status. At herd level, General Linear Models showed that pastoral production systems with transhumant herds had a higher bTB prevalence than sedentary herds. A model averaging analysis identified herd size, contact with wildlife, and the interaction of herd size and contact with wildlife as significant risk factors for bTB prevalence in cattle. A subsequent Structural Equation Model showed that the probability of contact with wildlife was influenced by herd size, through herd movement. Larger herds moved more and grazed in larger areas, hence the probability of grazing in an area with wildlife and contact with either infected cattle or infected wildlife hosts increased, enhancing the chances for bTB infection. Therefore, future bTB control strategies in cattle in

The Deep-Sea Polyextremophile Halobacteroides lacunaris TB21 Rough-Type LPS: Structure and Inhibitory Activity towards Toxic LPS

PubMed Central

Di Lorenzo, Flaviana; Palmigiano, Angelo; Paciello, Ida; Pallach, Mateusz; Garozzo, Domenico; Bernardini, Maria-Lina; La Cono, Violetta; Yakimov, Michail M.; Molinaro, Antonio; Silipo, Alba

2017-01-01

The structural characterization of the lipopolysaccharide (LPS) from extremophiles has important implications in several biomedical and therapeutic applications. The polyextremophile Gram-negative bacterium Halobacteroides lacunaris TB21, isolated from one of the most extreme habitats on our planet, the deep-sea hypersaline anoxic basin Thetis, represents a fascinating microorganism to investigate in terms of its LPS component. Here we report the elucidation of the full structure of the R-type LPS isolated from H. lacunaris TB21 that was attained through a multi-technique approach comprising chemical analyses, NMR spectroscopy, and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry. Furthermore, cellular immunology studies were executed on the pure R-LPS revealing a very interesting effect on human innate immunity as an inhibitor of the toxic Escherichia coli LPS. PMID:28653982

Structural Genomics of Protein Phosphatases

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

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less

Role of Ga particulates on the structure and optical properties of Y3(Al,Ga)5O12:Tb thin films prepared by PLD

NASA Astrophysics Data System (ADS)

Yousif, A.; Duvenhage, M. M.; Ntwaeaborwa, O. M.; Swart, H. C.

2018-04-01

Y3(Al,Ga)5O12:Tb thin films (70 nm) have been prepared by pulsed laser deposition on a Si (100) substrate at the substrate temperature of 300 °C. The effect of annealing time on the structural, morphological and luminescence properties of Y3(Al,Ga)5O12:Tb thin films at 800 °C were studied. The crystal structure of the samples was studied by X- ray diffraction (XRD) and showed shifts in the peak positions to lower diffraction angles for the annealed film compared to the XRD peak positions of the commercial Y3(Al,Ga)5O12:Tb powder. A new excitation band different from the original Y3(Al,Ga)5O12:Tb powder was also observed for the annealed films. The shift in the XRD pattern and the new excitation band for the annealed film suggested that the films were enriched with Ga after annealing.

Testing for TB Infection

MedlinePlus

... Search Form Controls Cancel Submit Search The CDC Tuberculosis (TB) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Tuberculosis Basic TB Facts How TB Spreads Latent TB ...

Prevalence of post-traumatic stress symptoms and associated factors in tuberculosis (TB), TB retreatment and/or TB-HIV co-infected primary public health-care patients in three districts in South Africa.

PubMed

Peltzer, Karl; Naidoo, Pamela; Matseke, Gladys; Louw, Julia; McHunu, Gugu; Tutshana, Bomkazi

2013-01-01

High rates of tuberculosis (TB) and TB/HIV co-infection is often linked with mental health issues such as post-traumatic stress disorder (PTSD) symptoms, which is further associated with poor health outcomes. In a country such as South Africa where rates of these infectious diseases are high, it is concerning that there is limited/no data on prevalence rates of mental disorders such as PTSD and its associated factors. Therefore, the aim of this study was to establish the prevalence of PTSD symptoms and associated factors in TB, TB retreatment and/or TB-HIV co-infected primary public health-care patients in three districts in South Africa. Brief screening self-report tools were used to measure: PTSD symptoms, psychological distress (anxiety and depression) and alcohol misuse. Other relevant measures, such as adherence to medication, stressful life events and sexual risk-taking behaviours, were obtained through structured questions. A total of 4900 public primary care adult patients from clinics in high TB burden districts from three provinces in South Africa participated. All the patients screened positive for TB (either new or retreatment cases). The prevalence of PTSD symptoms was 29.6%. Patients who screened positive for PTSD symptoms and psychological distress were more likely to be on antidepressant medication. Factors that predicted PTSD symptoms were poverty, residing in an urban area, psychological distress, suicide attempt, alcohol and/or drug use before sex, unprotected sex, TB-HIV co-infected and the number of other chronic conditions. Health-care systems should be strengthened to improve delivery of mental health care, by focusing on existing programmes and activities, such as those which address the prevention and treatment of TB and HIV.

Synthesis, structure, and photoluminescence properties of novel KBaSc2 (PO4 )3 :Ce(3+) /Eu(2+) /Tb(3+) phosphors for white-light-emitting diodes.

PubMed

Jiao, Mengmeng; Lü, Wei; Shao, Baiqi; Zhao, Lingfei; You, Hongpeng

2015-08-24

A series of novel KBaSc2 (PO4 )3 :Ce(3+) /Eu(2+) /Tb(3+) phosphors are prepared using a solid-state reaction. X-ray diffraction analysis and Rietveld structure refinement are used to check the phase purity and crystal structure of the prepared samples. Ce(3+) - and Eu(2+) -doped phosphors both have broad excitation and emission bands, owing to the spin- and orbital-allowed electron transition between the 4f and 5d energy levels. By co-doping the KBaSc2 (PO4 )3 :Eu(2+) and KBaSc2 (PO4 )3 :Ce(3+) phosphors with Tb(3+) ions, tunable colors from blue to green can be obtained. The critical distance between the Eu(2+) and Tb(3+) ions is calculated by a concentration quenching method and the energy-transfer mechanism for Eu(2+) →Tb(3+) is studied by utilizing the Inokuti-Hirayama model. In addition, the quantum efficiencies of the prepared samples are measured. The results indicate that KBaSc2 (PO4 )3 :Eu(2+) ,Tb(3+) and KBaSc2 (PO4 )3 :Ce(3+) ,Tb(3+) phosphors might have potential applications in UV-excited white-light-emitting diodes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetostructural phase transformations in Tb 1-x Mn 2

DOE PAGES

Zou, Junding; Paudyal, Durga; Liu, Jing; ...

2015-01-16

Magnetism and phase transformations in non-stoichiometric Tb 1-xMn 2 (x = 0.056, 0.039) have been studied as functions of temperature and magnetic field using magnetization, heat capacity, and X-ray powder diffraction measurements. Lowering the temperature, the compounds sequentially order ferrimagnetically and antiferromagnetically, and finally, exhibit spin reorientation transitions. Moreover, these structural distortions from room temperature cubic to low temperature rhombohedral structures occur at T N, and are accompanied by large volume changes reaching ~-1.27% and -1.42%, respectively. First principles electronic structure calculations confirm the phase transformation from the ferrimagnetic cubic structure to the antiferromagnetic rhombohedral structure in TbMn 2.

Determining the band alignment of TbAs:GaAs and TbAs:In 0.53Ga 0.47As

DOE PAGES

Bomberger, Cory C.; Vanderhoef, Laura R.; Rahman, Abdur; ...

2015-09-10

Here, we propose and systematically justify a band structure for TbAs nanoparticles in GaAs and In 0.53Ga 0.47As host matrices. Moreover, fluence-dependent optical-pump terahertz-probe measurements suggest the TbAs nanoparticles have a band gap and provide information on the carrier dynamics, which are determined by the band alignment. Spectrophotometry measurements provide the energy of optical transitions in the nanocomposite systems and reveal a large blue shift in the absorption energy when the host matrix is changed from In 0.53Ga 0.47As to GaAs. Finally, Hall data provides the approximate Fermi level in each system. From this data, we deduce that the TbAs:GaAsmore » system forms a type I (straddling) heterojunction and the TbAs:In 0.53Ga 0.47As system forms a type II (staggered) heterojunction.« less

Exploring workplace TB interventions with foreign-born Latino workers.

PubMed

Eggerth, Donald E; Keller, Brenna M; Flynn, Michael A

2018-05-15

Persons born outside the United States are more likely to be diagnosed with tuberculosis disease (TB) than native-born individuals. Foreign-born Latinos at risk of TB may be difficult to reach with public health interventions due to cultural and institutional barriers. Workplaces employing large concentrations of foreign-born Latinos may be useful locations for TB interventions targeting this high-risk population. This study used a two-phase approach to investigate the feasibility of workplace TB interventions. The first phase investigated employer knowledge of TB and receptiveness to allowing TB interventions in their businesses through 5 structured interviews. The second phase investigated foreign-born workers' knowledge of TB and their receptiveness to receiving TB interventions in their places of employment through 12 focus groups stratified by gender and education. Phase 1: Only 1 of the 5 employers interviewed had a high level of knowledge about TB, and three had no knowledge other than that TB was a disease that involved coughing. They were receptive to workplace TB interventions, but were concerned about lost productivity and customers finding out if an employee had TB. Phase 2: There was no observed differences in responses between gender and between the bottom two education groups, so the final analysis took place between a gender-combined lower education group and higher education group. The higher education group tended to have knowledge that was more accurate and to view TB as a disease associated with poverty. The lower education group tended to have more misconceptions about TB and more often expressed concern that their employers would not support worksite interventions. The results from both phases indicate that more TB education is needed among both foreign-born Latino workers and their employers. Obstacles to implementing workplace TB interventions include knowledge, potential productivity loss, employer liability, and perceived customer response

Multi-q crystal and magnetic structure in TbMnO3: Evidence for a Soliton-lattice

NASA Astrophysics Data System (ADS)

Aliouane, N.; Strempfer, J.; Caliebe, W.

2005-03-01

In TbMnO3, Mn-spins order with a sinusoidal antiferromagnetic (AF) propagation wave vector QMn=[0,k+/-q,l] (q˜0.288b^*) at TN(Mn)=41K. The propagation vector QMn varies with temperature on cooling until TLock(Mn) ˜30K, which coincides with a ferroelectric transition. In addition to QMn reflections we find magnetic reflections at 3QMn. Our X-ray measurements show that the magneto-elastic coupling gives rise to a structural modulation at twice the magnetic wavevector (2QMn). Field cooling the sample under a magnetic field oriented along the a-direction with H>9T shows that all magnetic wavevectors for Mn and Tb collapse to a single q structure with Q=[0,1/4,0], an up-up, down-down phase, and coincide with anomalies in the polarization. We argue that the temperature and field dependence of the magnetic and superlattice reflections are consistent with a soliton formalism which predicts a stable commensurate single q=1/4 phase [1]. [1] Kimura et al., PRB 68, 60403(2003).

Tuberculosis Facts - Exposure to TB

MedlinePlus

Tuberculosis (TB) Facts Exposure to TB What is TB? “TB” is short for a disease called tuberculosis. TB is spread through the air from one ... Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination

Tuberculosis Facts - Testing for TB

MedlinePlus

Tuberculosis (TB) Facts Testing for TB What is TB? “TB” is short for a disease called tuberculosis. TB is spread through the air from one ... Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination

The structure and evolution of angiosperm nuclear genomes.

PubMed

Bennetzen, J L

1998-04-01

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.

Insights into structural variations and genome rearrangements in prokaryotic genomes.

PubMed

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Paris-Sud yeast structural genomics pilot-project: from structure to function.

PubMed

Quevillon-Cheruel, Sophie; Liger, Dominique; Leulliot, Nicolas; Graille, Marc; Poupon, Anne; Li de La Sierra-Gallay, Inès; Zhou, Cong-Zhao; Collinet, Bruno; Janin, Joël; Van Tilbeurgh, Herman

2004-01-01

We present here the outlines and results from our yeast structural genomics (YSG) pilot-project. A lab-scale platform for the systematic production and structure determination is presented. In order to validate this approach, 250 non-membrane proteins of unknown structure were targeted. Strategies and final statistics are evaluated. We finally discuss the opportunity of structural genomics programs to contribute to functional biochemical annotation.

Public-private mix for TB and TB-HIV care in Lagos, Nigeria.

PubMed

Daniel, O J; Adedeji Adejumo, O; Abdur-Razzaq, H A; Ngozi Adejumo, E; Salako, A A

2013-09-01

Private and public tuberculosis (TB) treatment centres in Lagos State, Nigeria. To assess the contribution of private health care providers to TB and TB-HIV (human immunodeficiency virus) case finding in Lagos State. A retrospective review of programme data submitted to the Lagos State TB and Leprosy Control Programme in 2011 by public, private for-profit (PFP) and private not-for-profit (PNFP) health care providers. A total of 8425 TB cases were notified by 31 private (11 PFP and 20 PNFP) and 99 public health facilities in Lagos State. Overall, the private facilities were responsible for 10.3% (866/8425) of the total TB cases notified. The proportion of TB patients tested for HIV was respectively 86.2%, 53.1% and 96.5% among public, PFP and PNFP facilities. Overall, 22.4% of the TB patients were HIV-positive. The HIV positivity rate among public, PFP and PNFP facilities was respectively 23.8%, 7.8% and 9.9%. Uptake of cotrimoxazole preventive therapy was respectively 69.6%, 25% and 38.2% among public, PFP and PNFP facilities, while that of antiretroviral therapy was respectively 23.8%, 8.3% and 9.1% in public, PFP and PNFP facilities. There is a need to scale up collaboration with the private sector, and particularly PNFP health providers.

TB & HIV: the deadly intersection.

PubMed

MacDougall, D S

1999-05-01

About 2 billion people worldwide are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). TB is the leading cause of premature death in less industrialized countries, and 8 million more people become infected every year. The World Health Organization (WHO) declared TB a global emergency in 1993 and launched a series of prevention and vaccination programs. In spite of effective drug therapy and a vaccine, tuberculosis remains a major public health problem. The TB and HIV epidemics are closely intertwined, and the risk of TB disease progression is 100 times greater in HIV-positive individuals. TB is the leading cause of death among HIV-infected people worldwide, and virologic evidence suggests that the host immune response to TB may enhance HIV replication and accelerate the progression of HIV infection. The interaction between the two diseases was the subject of a conference called TB & HIV: Applying Advances to the Clinic, Public Health, and the World. Charts and tables show reported TB cases in the U.S., trends in TB cases among foreign-born persons in the U.S., and the country of origin for foreign-born persons with TB in the U.S. Several poster sessions from the conference are summarized. Strategies for dealing with the TB epidemic are outlined.

Tuberculosis Facts - TB Can Be Treated

MedlinePlus

Tuberculosis (TB) Facts TB Can Be Treated What is TB? “TB” is short for a disease called tuberculosis. TB is spread through the air from one ... Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination Page 1 of 2 TB Facts: TB ...

Tuberculosis Facts - You Can Prevent TB

MedlinePlus

Tuberculosis (TB) Facts You Can Prevent TB What is TB? “TB” is short for a disease called tuberculosis. TB is spread through the air from one ... Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination TB Facts: You Can Prevent TB What ...

Does the integration of TB medical services in the general hospital improve the quality of TB care? Evidence from a case study in China.

PubMed

Sun, Qiang; Yin, Jia; Yin, Xiao; Zou, Guanyang; Liang, Mingli; Zhong, Jieming; Walley, John; Wei, Xiaolin

2013-06-01

Moving the clinical services from tuberculosis (TB) dispensary to the integrated county hospital (called integrated approach) has been practiced in China; however, it is unknown the quality of TB care in the integrated approach and in the dispensary approach. A total of 202 new TB patients were investigated using structured questionnaires in three counties implementing the integrated approach and one county implementing the dispensary approach. The quality of TB care is measured based on success rate of treatment, medical expenditure, health system delay and second-line drug use. The integrated approach showed a high success treatment rate. The medical expenditure in the integrated approach was USD 432, significantly lower than that in the dispensary approach (Z = -5.771, P < 0.001). The integrated approach had a shorter health system delay (5 days) than the dispensary approach (32 days). Twenty-six percent of patients in integrated hospitals were prescribed with second-line TB drugs, significantly lower than that in the TB dispensary (47%, χ(2) = 7.452, P = 0.006). However, the medical expenditure, use of second-line anti-TB drug and liver-protection drugs indeed varied greatly across the three integrated hospitals. The integrated approach showed better quality of TB care, but the performance of the integrated hospitals varied greatly. A method to standardize TB treatment and management of this approach is urgent.

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the

Investigation of Structure of Gd and Tb Nuclei using STARS and LiBerACE

NASA Astrophysics Data System (ADS)

Bonniwell, Cain; Pauerstein, Ben; Allmond, J. M.; Beausang, C. W.

2009-10-01

This experiment, performed at Livermore Berkeley National Lab as a collaboration of Livermore, Berkeley, and the University of Richmond, was designed to investigate the structure of gadolinium and terbium nuclei using the P + 156Gd reaction at E beam = 27 MeV. The experimental design included use of the STARS system for detecting charged particles as well as the LiBerACE clover array for detecting gamma rays. The master gate was set to record particle-gamma as well as gamma-gamma coincidences. The data is currently being analyzed using the RADWARE escl8r software package which has allowed the creation of extensive level schemes for several Gd and Tb nuclei. So far the data suggests new gamma ray transitions as well as new energy states in 154Gd and 155Tb. The project is ongoing, and the results will be presented. This work was supported by the US Department of Energy under grant numbers DE-FG52NA26206 and DE-FG02-05ER41379.

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

PubMed

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

2016-08-05

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

Functional Insights from Structural Genomics

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

Forouhar,F.; Kuzin, A.; Seetharaman, J.

2007-01-01

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNAmore » methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).« less

[Preparation and luminescent properties of CaMoO4:Tb3+].

PubMed

Wang, Xi-gui; Bo, Su-ling; Na, Mi-la; Qi, Xia

2010-01-01

The precursor of the sample CaMoO4:Tb3+ was prepared by the coprecipitation method. TG-DTA spectra show that there is, at 850 degrees C, an energy absorption peak, suggesting that the sample reaches the activation spot of its response. The XRD pattern of the roasted sample shows that CaMoO4:Tb3+, in the single phase, is a representative scheelite structure of CaMoO4, but the peaks shift toward right, implying that tiny crystal defect in the crystal is produced. The defect is likely to be formed by the formation of the holes as two Tb3+ replace three Ca2+ in a cell. The excitation and emission spectra of the sample were investigated and revealed that the defect structure of the sample is in favor of the energy transfer of the characteristic peak (488 nm) of the MoO4(2-) effectively to Tb3+, and makes the 4f electrons of the Tb3+ transit, especially the (7)F6-->(5)D4 electronic transition (488 nm) of the Tb3+, to be greatly strengthened. As a result, the emission spectra with lamdaex=488 nm show that the emission intensity of the spontaneously activated fluorescence MoO4(2-) is greatly weakened, while the green light luminescence intensity of the (5)D4-->(7)F5 transition (544 nm) of the Tb3+ is greatly enhanced. This suggests that the sample CaMoO4:Tb3+ will become the luminescence material with potentially great application value.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

Genome Structure of the Legume, Lotus japonicus

PubMed Central

Sato, Shusei; Nakamura, Yasukazu; Kaneko, Takakazu; Asamizu, Erika; Kato, Tomohiko; Nakao, Mitsuteru; Sasamoto, Shigemi; Watanabe, Akiko; Ono, Akiko; Kawashima, Kumiko; Fujishiro, Tsunakazu; Katoh, Midori; Kohara, Mitsuyo; Kishida, Yoshie; Minami, Chiharu; Nakayama, Shinobu; Nakazaki, Naomi; Shimizu, Yoshimi; Shinpo, Sayaka; Takahashi, Chika; Wada, Tsuyuko; Yamada, Manabu; Ohmido, Nobuko; Hayashi, Makoto; Fukui, Kiichi; Baba, Tomoya; Nakamichi, Tomoko; Mori, Hirotada; Tabata, Satoshi

2008-01-01

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes. PMID:18511435

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

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

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

DOE PAGES

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; ...

2016-03-07

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Identification and characterization of potential druggable targets among hypothetical proteins of extensively drug resistant Mycobacterium tuberculosis (XDR KZN 605) through subtractive genomics approach.

PubMed

Uddin, Reaz; Siddiqui, Quratulain Nehal; Azam, Syed Sikander; Saima, Bibi; Wadood, Abdul

2018-03-01

Among the resistant isolates of tuberculosis (TB), the multidrug resistance tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) are the areas of growing concern for which the front-line antibiotics are no more effective. As a result, the search of new therapeutic targets against TB is an imperative need of time. On the other hand, the target identification is an a priori step in drug discovery based research. Furthermore, the availability of the complete proteomic data of extensively drug resistant Mycobacterium tuberculosis (XDR-MTB) made it possible to carry out in silico analysis for the discovery of new drug targets. In the current study, we aimed to prioritize the potential drug targets among the hypothetical proteins of XDR-TB via subtractive genomics approach. In the subtractive genomics, we stepwise reduced the complete proteome of XDR-MTB to only two hypothetical proteins and evidently proposed them as new therapeutic targets. The 3D structure of one of the two target proteins was predicted via homology modeling and later on, validated by various analysis tools. Our study suggested that the domains identified and the motif hits found in the sequences of the shortlisted drug targets are crucial for the survival of the XDR-MTB. To the best of our knowledge, the current study is the first attempt in which the complete proteomic data of XDR-MTB was subjected to the computational subtractive genomics approach and therefore, would provide an opportunity to identify the unique therapeutic targets against deadly XDR-MTB. Copyright © 2017 Elsevier B.V. All rights reserved.

Questions and Answers about TB

MedlinePlus

... Search Form Controls Cancel Submit Search The CDC Tuberculosis (TB) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Tuberculosis Basic TB Facts How TB Spreads Latent TB ...

HIV and Tuberculosis (TB)

MedlinePlus

... or brain. If not treated, TB disease can cause death. HIV weakens the immune system , increasing the risk ... spine, or brain. If not treated, TB can cause death. How does TB spread from person to person? ...

Magnetic Correlations in the Triangular Antiferromagnet TbInO3

NASA Astrophysics Data System (ADS)

Sala, Gabriele; Clark, Lucy; Maharaj, Dalini; Stone, Matthew B.; Knight, Kevin S.; Cheong, Sang-Wook; Gaulin, Bruce D.

TbInO3 crystallizes with a hexagonal P63 cm structure in which layers of edge-sharing triangles of magnetic Tb3+ ions are separated by non-magnetic [InO5]7- units. TbInO3, therefore, realizes an excellent opportunity to explore the behavior of a two-dimensional magnetic triangular lattice, a canonical model of geometric frustration. Here we present our study of a polycrystalline sample of TbInO3. Our high resolution powder neutron diffraction data (HRPD, ISIS) of TbInO3 confirm that the triangular layers of Tb3+ remain undistorted to at least 0 . 46 K. Magnetic susceptibility data follow Curie-Weiss behavior over a wide range of T with θ = - 17 . 19 (3) K indicating the dominance of antiferromagnetic correlations. The susceptibility data also show an absence of conventional long-range spin order down to at least 0 . 55 K, reflecting the frustrated nature of TbInO3. Elastic magnetic diffuse neutron scattering (SEQUOIA, SNS) is observed below ~ 15 K, due to the presence of static two-dimensional spin correlations. The spectrum of crystal field excitations in TbInO3 appears to have an exotic form due to the existence of two crystallographically distinct Tb3+ sites and leads to a strong Ising anisotropy of the spin symmetry.

The Divided Bacterial Genome: Structure, Function, and Evolution.

PubMed

diCenzo, George C; Finan, Turlough M

2017-09-01

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella , Vibrio , and Burkholderia . The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure. Copyright © 2017 American Society for Microbiology.

Prevalence of latent TB infection and TB disease among adolescents in high TB burden countries in Africa: a systematic review protocol.

PubMed

Bunyasi, Erick Wekesa; Schmidt, Bey-Marrie; Abdullahi, Leila Hussein; Mulenga, Humphrey; Tameris, Michele; Luabeya, Angelique; Shenje, Justin; Scriba, Thomas; Geldenhuys, Hennie; Wood, Robin; Hatherill, Mark

2017-03-10

Almost a third of the world population has latent tuberculosis (TB) infection (LTBI), ∼10 million of whom develop TB disease annually, despite existence of effective, but lengthy, preventive and curative drug regimens. Although adolescents appear to have a very high force of LTBI, their reported incidence of TB disease is less than that of their corresponding general population. The few available studies on adolescent TB infection and disease prevalence are not sufficient to address the apparent discordance between rates of infection and disease in high TB burden countries in Africa. Therefore, we aim to perform a systematic review to examine the relationship between adolescent LTBI and TB disease, benchmarked against national TB disease burden data. A comprehensive literature search will be performed for cross-sectional studies and screening data in cohort studies to determine the prevalence of LTBI and TB disease among adolescents in high TB burden countries in Africa in the following databases: PubMed , Scopus , Cochrane library , Web of Science , Africa Wide , CINAHL and the Africa Index Medicus . This will be supplemented by a search of reference lists of selected articles for potentially relevant articles. We will restrict our search to articles published in the English language between 1990 and 2016 among adolescents in order to obtain estimates reflective of the mature HIV epidemic in most high TB burden countries in Africa that occurred over this critical period. Primary end points are: prevalence of LTBI and TB disease. We will use the random-effects or fixed-effects modelling for our meta-analysis based on heterogeneity estimates. No ethics approval is required given that this is a systematic review. Findings will be disseminated in a peer-reviewed journal in line with the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). CRD42015023495. Published by the BMJ Publishing Group Limited. For permission to use (where not already

46 CFR 36.05-10 - Protection of personnel-TB/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Protection of personnel-TB/ALL. 36.05-10 Section 36.05-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS ELEVATED TEMPERATURE CARGOES Cargo Tanks § 36.05-10 Protection of personnel—TB/ALL. (a) Decks, bulkheads, or other structures shall...

46 CFR 36.05-10 - Protection of personnel-TB/ALL.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Protection of personnel-TB/ALL. 36.05-10 Section 36.05-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS ELEVATED TEMPERATURE CARGOES Cargo Tanks § 36.05-10 Protection of personnel—TB/ALL. (a) Decks, bulkheads, or other structures shall...

Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a TBNET/RESIST-TB consensus statement.

PubMed

Domínguez, J; Boettger, E C; Cirillo, D; Cobelens, F; Eisenach, K D; Gagneux, S; Hillemann, D; Horsburgh, R; Molina-Moya, B; Niemann, S; Tortoli, E; Whitelaw, A; Lange, C

2016-01-01

The emergence of drug-resistant strains of Mycobacterium tuberculosis is a challenge to global tuberculosis (TB) control. Although culture-based methods have been regarded as the gold standard for drug susceptibility testing (DST), molecular methods provide rapid information on mutations in the M. tuberculosis genome associated with resistance to anti-tuberculosis drugs. We ascertained consensus on the use of the results of molecular DST for clinical treatment decisions in TB patients. This document has been developed by TBNET and RESIST-TB groups to reach a consensus about reporting standards in the clinical use of molecular DST results. Review of the available literature and the search for evidence included hand-searching journals and searching electronic databases. The panel identified single nucleotide mutations in genomic regions of M. tuberculosis coding for katG, inhA, rpoB, embB, rrs, rpsL and gyrA that are likely related to drug resistance in vivo. Identification of any of these mutations in clinical isolates of M. tuberculosis has implications for the management of TB patients, pending the results of in vitro DST. However, false-positive and false-negative results in detecting resistance-associated mutations in drugs for which there is poor or unproven correlation between phenotypic and clinical drug resistance complicate the interpretation. Reports of molecular DST results should therefore include specific information on the mutations identified and provide guidance for clinicians on interpretation and on the choice of the appropriate initial drug regimen.

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

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

Bhagavat, Raghu; Kim, Heung -Bok; Kim, Chang -Yub

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived frommore » a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.« less

A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

DOE PAGES

Bhagavat, Raghu; Kim, Heung -Bok; Kim, Chang -Yub; ...

2017-10-02

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived frommore » a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.« less

Optimized guide RNA structure for genome editing via Cas9

PubMed Central

Xu, Jianyong; Lian, Wei; Jia, Yuning; Li, Lingyun; Huang, Zhong

2017-01-01

The genome editing tool Cas9-gRNA (guide RNA) has been successfully applied in different cell types and organisms with high efficiency. However, more efforts need to be made to enhance both efficiency and specificity. In the current study, we optimized the guide RNA structure of Streptococcus pyogenes CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system to improve its genome editing efficiency. Comparing with the original functional structure of guide RNA, which is composed of crRNA and tracrRNA, the widely used chimeric gRNA has shorter crRNA and tracrRNA sequence. The deleted RNA sequence could form extra loop structure, which might enhance the stability of the guide RNA structure and subsequently the genome editing efficiency. Thus the genome editing efficiency of different forms of guide RNA was tested. And we found that the chimeric structure of gRNA with original full length of crRNA and tracrRNA showed higher genome editing efficiency than the conventional chimeric structure or other types of gRNA we tested. Therefore our data here uncovered the new type of gRNA structure with higher genome editing efficiency. PMID:29212218

Difference Between Latent TB Infection and Active TB Disease

MedlinePlus

... chest x-ray, or positive sputum smear or culture • • Has active TB bacteria in his/her body • • Usually feels sick and may have symptoms such as coughing, fever, and weight loss • • May spread TB bacteria to others • • Needs treatment ...

Use of whole genome sequencing in surveillance of drug resistant tuberculosis.

PubMed

McNerney, Ruth; Zignol, Matteo; Clark, Taane G

2018-05-01

The threat of resistance to anti-tuberculosis drugs is of global concern. Current efforts to monitor resistance rely on phenotypic testing where cultured bacteria are exposed to critical concentrations of the drugs. Capacity for such testing is low in TB endemic countries. Drug resistance is caused by mutations in the Mycobacterium tuberculosis genome and whole genome sequencing to detect these mutations offers an alternative means of assessing resistance. Areas covered: The challenges of assessing TB drug resistance are discussed. Progress in elucidating the M. tuberculosis resistome and evidence of the accuracy of next generation sequencing for detecting resistance is reviewed. Expert Commentary: There are considerable advantages to using next generation sequencing for TB drug resistance surveillance. Accuracy is high for detecting resistance to the major first-line drugs but is currently lower for the second-line drugs due to our incomplete knowledge regarding resistance causing mutations. With the advances in sequencing technology and the opportunity to replace phenotypic drug susceptibility testing with safer and more cost effective methods it would appear that the question is when to implement. Current bottlenecks are sample extraction to allow whole genome sequencing directly from sputum and the lack of bioinformatics expertise in some TB endemic countries.

Structural genomic variations and Parkinson's disease.

PubMed

Bandrés-Ciga, Sara; Ruz, Clara; Barrero, Francisco J; Escamilla-Sevilla, Francisco; Pelegrina, Javier; Vives, Francisco; Duran, Raquel

2017-10-01

Parkinson's disease (PD) is the second most common neurodegenerative disease, whose prevalence is projected to be between 8.7 and 9.3 million by 2030. Until about 20 years ago, PD was considered to be the textbook example of a "non-genetic" disorder. Nowadays, PD is generally considered a multifactorial disorder that arises from the combination and complex interaction of genes and environmental factors. To date, a total of 7 genes including SNCA, LRRK2, PARK2, DJ-1, PINK 1, VPS35 and ATP13A2 have been seen to cause unequivocally Mendelian PD. Also, variants with incomplete penetrance in the genes LRRK2 and GBA are considered to be strong risk factors for PD worldwide. Although genetic studies have provided valuable insights into the pathogenic mechanisms underlying PD, the role of structural variation in PD has been understudied in comparison with other genomic variations. Structural genomic variations might substantially account for such genetic substrates yet to be discovered. The present review aims to provide an overview of the structural genomic variants implicated in the pathogenesis of PD.

Fine mapping of powdery mildew resistance genes PmTb7A.1 and PmTb7A.2 in Triticum boeoticum (Boiss.) using the shotgun sequence assembly of chromosome 7AL.

PubMed

Chhuneja, Parveen; Yadav, Bharat; Stirnweis, Daniel; Hurni, Severine; Kaur, Satinder; Elkot, Ahmed Fawzy; Keller, Beat; Wicker, Thomas; Sehgal, Sunish; Gill, Bikram S; Singh, Kuldeep

2015-10-01

A novel powdery mildew resistance gene and a new allele of Pm1 were identified and fine mapped. DNA markers suitable for marker-assisted selection have been identified. Powdery mildew caused by Blumeria graminis is one of the most important foliar diseases of wheat and causes significant yield losses worldwide. Diploid A genome species are an important genetic resource for disease resistance genes. Two powdery mildew resistance genes, identified in Triticum boeoticum (A(b)A(b)) accession pau5088, PmTb7A.1 and PmTb7A.2 were mapped on chromosome 7AL. In the present study, shotgun sequence assembly data for chromosome 7AL were utilised for fine mapping of these Pm resistance genes. Forty SSR, 73 resistance gene analogue-based sequence-tagged sites (RGA-STS) and 36 single nucleotide polymorphism markers were designed for fine mapping of PmTb7A.1 and PmTb7A.2. Twenty-one RGA-STS, 8 SSR and 13 SNP markers were mapped to 7AL. RGA-STS markers Ta7AL-4556232 and 7AL-4426363 were linked to the PmTb7A.1 and PmTb7A.2, at a genetic distance of 0.6 and 6.0 cM, respectively. The present investigation established that PmTb7A.1 is a new powdery mildew resistance gene that confers resistance to a broad range of Bgt isolates, whereas PmTb7A.2 most probably is a new allele of Pm1 based on chromosomal location and screening with Bgt isolates showing differential reaction on lines with different Pm1 alleles. The markers identified to be linked to the two Pm resistance genes are robust and can be used for marker-assisted introgression of these genes to hexaploid wheat.

Anisotropy induced anomalies in Dy 1$-$xTb xAl 2

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

Khan, M.; Miami Univ., Oxford, OH; Pathak, A. K.

2017-01-02

The Dy 1$-$xTb xAl 2 alloys have been investigated by X-ray powder diffraction, heat capacity, and magnetic measurements. All samples exhibit cubic Laves phase crystal structure at room temperature but at T C, DyAl2 and TbAl 2 show tetragonal and rhombohedral distortions, respectively. First order phase transitions are observed below T C (at the spin-reorientation transition, T SR) in the alloys with 0.15 ≤ x ≤ 0.35. These transitions are signified by sharp heat capacity peaks and corresponding anomalies in the magnetization and ac magnetic susceptibility data. The observations are interpreted by taking into consideration the differences in easy magnetizationmore » directions of DyAl 2 and TbAl 2. Due to the competing magnetic structures, the anisotropy-related instability and magnetic frustrations are prominent in the Dy 1$-$xTb xAl 2 alloys at certain concentrations resulting in the first order transitions.« less

Staying on Track with TB Medicine

MedlinePlus

... medicines. If you have TB disease , you must remember that TB germs die very slowly. Even if you feel better after a few weeks on the TB medicines, it does not mean all the TB germs are dead. Treating TB takes months. Staying on your medicine the ... points to remember: • Anyone can breathe in TB germs and get ...

Tuberculosis Facts - TB and HIV/AIDS

MedlinePlus

Tuberculosis (TB) Facts TB and HIV/AIDS What is TB? “TB” is short for a disease called tuberculosis. TB is spread through the air from one ... Viral Hepatitis, STD, and TB Prevention Division of Tuberculosis Elimination

Structure, thermal and luminescence properties of Eu/Tb(BA)3phen/PAN fibers fabricated by electrospinning

NASA Astrophysics Data System (ADS)

Wang, Shiwei; Xie, Guangbo; Zhang, Jingjing; Zhang, Sen; Li, Tingju

2018-04-01

Novel high luminescence fibers often exhibit potential applications in the fields of color displays and sensor systems. In this study, Eu(BA)3phen and Tb(BA)3phen powders was successfully synthesized by solvothermal reactions, firstly. Then, three kinds of novel flexible Eu(BA)3phen/PAN, Tb(BA)3phen/PAN and Eu/Tb(BA)3phen/PAN (BA = benzoic acid, phen = phenanthroline, PAN = Polyacrylonitrile) fibers had been successfully prepared by electrospinning technology. The characterizations of the final products have been investigated in detail. It was found that the diameter of the as-prepared fibers were almost uniform with the fabricated complexes doping into PAN successfully. Thermogravimetric analysis indicates that the thermal stability of the pure PAN fiber could be improved by the incorporation of the complex, although only 1 wt % was added. Furthermore, in Eu/Tb(BA)3phen complex, the fluorescence intensity of Eu3+ ions was remarkably increased by adding Tb3+ ions. This is primarily due to an energy transfer from the 5D4 level of Tb (III) to the 5D0 level of Eu (III) ions, where Tb3+ acted as sensitizer. The corresponding luminescent fibers displayed the same regularity as the complexes. Moreover, with the increasing of the incorporation of complexes into PAN, the fluorescence intensities were significantly enhanced and reached its maximum value at 2.5 wt % for Eu(BA)3phen/PAN fibers and 2.0 wt% for Tb(BA)3phen/PAN fibers. The further intensity decreased with the increasing content of the complexes because of typical emission concentration quenching.

Identification of structural variation in mouse genomes.

PubMed

Keane, Thomas M; Wong, Kim; Adams, David J; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

Effect of different surfactants on structural and optical properties of Ce3+ and Tb3+ co-doped BiPO4 nanostructures

NASA Astrophysics Data System (ADS)

Lakshminarayana, G.; Dao, T. D.; Chen, K.; Sharma, Manoj; Takeda, T.; Brik, M. G.; Kityk, I. V.; Singh, Sarabjot; Nagao, T.

2015-01-01

In this paper we report on the Ce3+ and Tb3+ ions co-doped bismuth phosphate (BiPO4) nanostructures that were synthesized by a simple precipitation method using different surfactants such as glycerol/H2O, glycerol/ethylene glycol, oleic acid, and ethylene glycol. The structural (X-ray diffraction, scanning electron microscopy, tunneling electron microscopy), functional groups analysis (Fourier transform infrared and Raman spectroscopy), thermal (thermogravimetry and differential thermal analysis), and optical (photoluminescence, photoluminescence-excitation) properties were investigated. The structural and morphological analysis confirms the pure hexagonal crystal structure of the synthesized nanostructures. From the measured Fourier transform infrared (FTIR) and Raman spectra various functional groups such as υ3 stretching vibration of the PO4 group, and δ(O-P-O) and υ4 (PO4) vibrations including the υ2 and υ1 bending modes of the PO4 units are identified. Based on the thermal analysis, for all the studied samples an exothermic peak between 680 °C and 700 °C was observed due to phase transition from hexagonal to high temperature monoclinic. The Ce3+and Tb3+ codoped samples show spectrally broad 5d → 4f luminescence in the blue (centered at 459 nm) wavelength region under the direct optical excitation of Ce3+ at 417 nm. Similarly, Tb3+ has revealed four main emission bands (5D4 → 7F6, 5, 4 and 3) at 490 nm, 545 nm, 585 nm and 621 nm with 378 nm (7F6 → 5G6) as the excitation wavelength, including three more weak emission bands at 647 nm, 669 nm, and 681 nm which could be assigned to 5D4 → 7F2, 1, 0 emission transitions. Among them, 545 nm (5D4 → 7F5) has shown bright green emission. The Ce3+ and Tb3+ codoped sample synthesized with pure oleic acid have shown relatively high green emission intensity for Tb3+, and relatively weak blue emission intensity for Ce3+ under their respective optical excitation wavelengths.

Multi-scale structural community organisation of the human genome.

PubMed

Boulos, Rasha E; Tremblay, Nicolas; Arneodo, Alain; Borgnat, Pierre; Audit, Benjamin

2017-04-11

Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.

Management of MDR-TB in HIV co-infected patients in Eastern Europe: Results from the TB:HIV study.

PubMed

Efsen, A M W; Schultze, A; Miller, R F; Panteleev, A; Skrahin, A; Podlekareva, D N; Miro, J M; Girardi, E; Furrer, H; Losso, M H; Toibaro, J; Caylà, J A; Mocroft, A; Lundgren, J D; Post, F A; Kirk, O

2018-01-01

Mortality among HIV patients with tuberculosis (TB) remains high in Eastern Europe (EE), but details of TB and HIV management remain scarce. In this prospective study, we describe the TB treatment regimens of patients with multi-drug resistant (MDR) TB and use of antiretroviral therapy (ART). A total of 105 HIV-positive patients had MDR-TB (including 33 with extensive drug resistance) and 130 pan-susceptible TB. Adequate initial TB treatment was provided for 8% of patients with MDR-TB compared with 80% of those with pan-susceptible TB. By twelve months, an estimated 57.3% (95%CI 41.5-74.1) of MDR-TB patients had started adequate treatment. While 67% received ART, HIV-RNA suppression was demonstrated in only 23%. Our results show that internationally recommended MDR-TB treatment regimens were infrequently used and that ART use and viral suppression was well below the target of 90%, reflecting the challenging patient population and the environment in which health care is provided. Urgent improvement of management of patients with TB/HIV in EE, in particular for those with MDR-TB, is needed and includes widespread access to rapid TB diagnostics, better access to and use of second-line TB drugs, timely ART initiation with viral load monitoring, and integration of TB/HIV care. Copyright © 2017 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Controllable synthesis of Ln3+ (Ln = Tb, Eu) doped zinc phosphate nano-/micro-structured materials: phase, morphology and luminescence properties

NASA Astrophysics Data System (ADS)

Yue, Dan; Lu, Wei; Li, Chunyang; Zhang, Xinlei; Liu, Chunxia; Wang, Zhenling

2014-01-01

Ln3+ (Ln = Tb, Eu) doped zinc phosphate tetrahydrate (ZPT:Ln3+) and ammonium zinc phosphate (AZP:Ln3+) nano-/micro-structured materials were synthesized in aqueous solution without the addition of any structure-directing agent. The phase structures, morphologies and luminescence properties of the as-synthesized samples were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), photoluminescence (PL) spectroscopy and lifetime. These investigations indicate that different phosphate sources MnH(3-n)PO4 (M = NH4+ or Na+, n = 1, 2, 3) can lead to the altering of morphology from nanosheet to microflower, but have no significant effect on the phase structure of the samples. The microlump, nanosheet, and microflower (constructed by the primary microlumps or nanosheets) of orthorhombic ZPT:Ln3+ could be selectively prepared by adjusting the pH value from 3.5 to 7.0. A mixture of orthorhombic ZPT:Ln3+ and monoclinic AZP:Ln3+ with a microflower morphology was obtained when the pH value was adjusted to 8.0. Monoclinic AZP:Ln3+ microplate, microcube and nanoparticle morphologies were obtained at pH values of 8.5, 9.0 and 11.0 respectively. The phase transformation and growth mechanism of the diverse morphologies were proposed, and ZPT:Ln3+ (Ln3+ = Eu or Tb) samples exhibit red or green emission under the excitation of UV light.Ln3+ (Ln = Tb, Eu) doped zinc phosphate tetrahydrate (ZPT:Ln3+) and ammonium zinc phosphate (AZP:Ln3+) nano-/micro-structured materials were synthesized in aqueous solution without the addition of any structure-directing agent. The phase structures, morphologies and luminescence properties of the as-synthesized samples were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), photoluminescence (PL) spectroscopy and lifetime. These

Genome Pool Strategy for Structural Coverage of Protein Families

PubMed Central

Jaroszewski, Lukasz; Slabinski, Lukasz; Wooley, John; Deacon, Ashley M.; Lesley, Scott A.; Wilson, Ian. A.; Godzik, Adam

2010-01-01

As noticed by generations of structural biologists, closely homologous proteins may have substantially different crystallization properties and propensities. These observations can be used to systematically introduce additional dimensionality into crystallization trials by targeting homologous proteins from multiple genomes in a “genome pool” strategy. Through extensive use of our recently introduced “crystallization feasibility score” (Slabinski et al., 2007a), we can explain that the genome pool strategy works well because the crystallization feasibility scores are surprisingly broad within families of homologous proteins, with most families containing a range of optimal to very difficult targets. We also show that some families can be regarded as relatively “easy”, where a significant number of proteins are predicted to have optimal crystallization features, and others are “very difficult”, where almost none are predicted to result in a crystal structure. Thus, the outcome of such variable distributions of such crystallizability' preferences leads to uneven structural coverage of known families, with “easier” or “optimal” families having several times more solved structures than “very difficult” ones. Nevertheless, this latter category can be successfully targeted by increasing the number of genomes that are used to select targets from a given family. On average, adding 10 new genomes to the “genome pool” provides more promising targets for 7 “very difficult” families. In contrast, our crystallization feasibility score does not indicate that any specific microbial genomes can be readily classified as “easier” or “very difficult” with respect to providing suitable candidates for crystallization and structure determination. Finally, our analyses show that specific physicochemical properties of the protein sequence favor successful outcomes for structure determination and, hence, the group of proteins with known 3D

Latent TB infection and pulmonary TB disease among patients with diabetes mellitus in Bandung, Indonesia.

PubMed

Koesoemadinata, Raspati C; McAllister, Susan M; Soetedjo, Nanny N M; Febni Ratnaningsih, Dwi; Ruslami, Rovina; Kerry, Sarah; Verrall, Ayesha J; Apriani, Lika; van Crevel, Reinout; Alisjahbana, Bachti; Hill, Philip C

2017-02-01

Screening and treatment of latent TB infection (LTBI) and TB disease could reduce diabetes mellitus (DM)-associated TB. We aimed to describe the prevalence of LTBI and pulmonary TB among patients with DM in a TB-endemic setting. Patients with DM attending a hospital and community centres in Bandung, Indonesia, underwent LTBI screening using interferon gamma release assay (IGRA). TB was investigated by sputum smear, culture and x-ray. TB contacts from a parallel study were age- and sex-matched to patients with DM to compare LTBI and TB disease prevalence. Of 682 patients with DM screened, 651 (95.5%) were eligible. Among 'TB disease-free' patients, LTBI prevalence was 38.9% (206/530; 95% CI 34.7-43.2). Patients with DM were less likely to be IGRA positive than TB contacts (38.6%, 54/140; 95% CI 30.5-46.6 vs 68.6%, 96/140; 95% CI 60.9-72.3: p<0.001); but had a higher disease prevalence (4.9%, 8/164; 95% CI 1.6-8.2 vs 1.2%, 2/164; 95% CI -0.5 to 2.9: p=0.054). Patients with DM in crowded households had increased risk of LTBI (AOR 1.71; 95% CI 1.19-2.45). LTBI prevalence in patients with DM was lower than in household contacts, but patients with DM were more likely to have TB disease. Further studies should explore possible benefits of LTBI screening and preventive therapy in patients with DM in TB-endemic settings. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Thermally stimulated properties in ZnSe:Tb and ZnSe:(Mn, Tb) phosphors

NASA Astrophysics Data System (ADS)

Mishra, A. K.; Mishra, S. K.; Pandey, S. P.; Lakshmi Mishra, Kshama

2018-02-01

Thermoluminescence studies were performed of ZnSe:Tb and ZnSe:(Mn, Tb) phosphors. A method of preparation for ZnSe phosphors doped with Tb and (Mn, Tb) has been discussed. The thermoluminescence (TL) properties of these phosphors have been studied from 100 to 370 K temperature after exciting by UV radiation (365 nm) at three uniform heating rates 0.4, 0.6 and 0.9 K/s. The trapping parameters like trap depth, lifetime of electrons and capture cross-section have also been determined using various methods.

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data.

PubMed

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data.

NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data

PubMed Central

Seol, Young-Joo; Lee, Tae-Ho; Park, Dong-Suk; Kim, Chang-Kug

2016-01-01

The National Agricultural Biotechnology Information Center developed an access portal to search, visualize, and share agricultural genomics data with a focus on South Korean information and resources. The portal features an agricultural biotechnology database containing a wide range of omics data from public and proprietary sources. We collected 28.4 TB of data from 162 agricultural organisms, with 10 types of omics data comprising next-generation sequencing sequence read archive, genome, gene, nucleotide, DNA chip, expressed sequence tag, interactome, protein structure, molecular marker, and single-nucleotide polymorphism datasets. Our genomic resources contain information on five animals, seven plants, and one fungus, which is accessed through a genome browser. We also developed a data submission and analysis system as a web service, with easy-to-use functions and cutting-edge algorithms, including those for handling next-generation sequencing data. PMID:26848255

Exploiting Genome Structure in Association Analysis

PubMed Central

Kim, Seyoung

2014-01-01

Abstract A genome-wide association study involves examining a large number of single-nucleotide polymorphisms (SNPs) to identify SNPs that are significantly associated with the given phenotype, while trying to reduce the false positive rate. Although haplotype-based association methods have been proposed to accommodate correlation information across nearby SNPs that are in linkage disequilibrium, none of these methods directly incorporated the structural information such as recombination events along chromosome. In this paper, we propose a new approach called stochastic block lasso for association mapping that exploits prior knowledge on linkage disequilibrium structure in the genome such as recombination rates and distances between adjacent SNPs in order to increase the power of detecting true associations while reducing false positives. Following a typical linear regression framework with the genotypes as inputs and the phenotype as output, our proposed method employs a sparsity-enforcing Laplacian prior for the regression coefficients, augmented by a first-order Markov process along the sequence of SNPs that incorporates the prior information on the linkage disequilibrium structure. The Markov-chain prior models the structural dependencies between a pair of adjacent SNPs, and allows us to look for association SNPs in a coupled manner, combining strength from multiple nearby SNPs. Our results on HapMap-simulated datasets and mouse datasets show that there is a significant advantage in incorporating the prior knowledge on linkage disequilibrium structure for marker identification under whole-genome association. PMID:21548809

Interleukin-1 receptor antagonist, a biomarker of response to anti-TB treatment in HIV/TB co-infected patients.

PubMed

Nouhin, Janin; Pean, Polidy; Madec, Yoann; Chevalier, Mathieu F; Didier, Celine; Borand, Laurence; Blanc, François-Xavier; Scott-Algara, Daniel; Laureillard, Didier; Weiss, Laurence

2017-05-01

Despite the high frequency of tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) in human immunodeficiency virus (HIV)/TB co-infected patients, no diagnostic test is available. Here, we investigated whether monocyte/macrophage activation markers can predict TB-IRIS occurrence and if they are modulated by anti-TB treatment. Frozen plasma was obtained from 127 HIV/TB co-infected adults naïve for antiretroviral therapy, enrolled in the CAMELIA trial, 36 of whom developed TB-IRIS. Concentrations of IL-1Ra, sCD14, and sCD163 were measured at anti-TB treatment onset (baseline), after 8 weeks of anti-TB treatment and at TB-IRIS time. At baseline, IL-1Ra and sCD14 concentrations were similar in TB-IRIS and non-IRIS patients. sCD163 concentrations, although significantly higher in TB-IRIS patients, did not remain associated with TB-IRIS occurrence in multivariate analysis. At the time of TB-IRIS, patients displayed higher concentrations of IL-1Ra (p = 0.002) and sCD14 (p < 0.001). The most striking result was the significant decrease in IL-1Ra after 8 weeks of anti-TB treatment (median reduction: -63% (p < 0.0001)). None of the biomarkers tested was associated with TB-IRIS occurrence. However, repeated measurement of IL-1Ra could help for the diagnosis of TB-IRIS. The substantial reduction of IL-1Ra under treatment suggests that IL-1Ra could be a surrogate biomarker of anti-TB treatment response in HIV-infected patients. Copyright © 2017 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Magnetic and thermal properties of amorphous TbFeCo alloy films

NASA Astrophysics Data System (ADS)

Wang, Ke; Dong, Shuo; Huang, Ya; Qiu, Yuzhen

2017-07-01

Amorphous TbFeCo material with perpendicular magnetic anisotropy is currently attracting more attention for potential applications in spintronic devices and logic memories. We systematically investigate magnetic, structural, thermal, optical and electrical properties of TbFeCo alloy films. It shows out-of-plane easy axis of the films turns into in-plane orientation after annealing. Significant increase in saturation magnetization in the temperature range between 400 and 450 °C is revealed by thermomagnetic measurements. The occurrence of crystallization and oxidation at high temperatures is confirmed by X-ray diffraction measurements. Pronounced changes in optical reflectance and sheet resistance are observed with temperature, in line with structural relaxation and change. The activation barriers for crystallization and oxidation are determined to be 1.01 eV and 0.83 eV, respectively, for FeCo-rich and Tb-rich samples. Better thermal stability against crystallization and oxidation is demonstrated in the FeCo-rich sample than the Tb-rich type. Our results provide some useful information for the alloy used in device fabrication.

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

[Genome instability in pulmonary tuberculosis before and after treatment].

PubMed

Dzhokhadze, T A; Buadze, T Zh; Rubanov, K Dzh; Kiriia, N A; Lezhava, T A

2013-11-01

Pulmonary tuberculosis is classified as a disease with a genetic predisposition, and therefore, as with other pathologies related to this group of diseases, by pulmonary tuberculosis, special importance is given to finding those markers that enable early identification of risk groups, such as skrinnig in general population and relatives of patients with tuberculosis, which in turn can provide the basis for preventive measures. One of this markers is the level of genome stability. The aim of this study was a comparative evaluation of the functional parameters of the genome variability in patients with sensitive form of pulmonary tuberculosis before and after treatment, and the possibility of its correction with anti-stress peptide bioregulator - epitalon. The studies were conducted using short-term mitoge -stimulated cell cultures of TB patients, before and after treatment. As an indicator of genome stability has been studied the frequency of structural and numerical chromosome aberrations and fragile sites. It is shown, that in intact cultures from patients with pulmonary tuberculosis, before treatment was significantly higher level of frequency of cells with structural chromosome aberrations, that still retained after the treatment. As for epithalon, it appears that was shown a pronounced protective effect after treatment, on the test of chromosome aberrations, by reducing both overall mean frequency aberrant cells and indicators for all individuals. In the study of fragility of chromosomes in patients with primary tuberculosis was found, that in intact cultures, the proportion of cells with chromosomal fragile sites was higher than in control group of healthy individuals, befor and after treatment. High frequency of chromosome fragility persisted by treatment with peptide bioregulator in both cases - before and after treatment. It is suggested that the identified patterns can be correlated with a high incidence of re- TB.

Synthesis, Structure, White-Light Emission, and Temperature Recognition Properties of Eu/Tb Mixed Coordination Polymers.

PubMed

An, Ran; Zhao, Hui; Hu, Huai-Ming; Wang, Xiaofang; Yang, Meng-Lin; Xue, Ganglin

2016-01-19

Two series of Eu(III)/Tb(III) coordination polymers, [LnL(glu)]n·2nH2O (Ln = Eu (1), Tb (2)) and [LnL(glu)(H2O)]n (Ln = Eu (3), Tb (4)) [HL = (2-(2-sulfophenyl)imidazo(4,5-f)(1,10)-phenanthroline, H2glu = glutaric acid] have been hydrothermally synthesized by controlling the pH values and characterized by elemental analysis, infrared spectra, and single-crystal X-ray diffraction. Isomorphic compounds 1 and 2 exhibit 6-connected 3D network with the pcu topological net, containing left- and right-handed helical chains. Isomorphic compounds 3 and 4 show 3,4-connected 2D new topology with the point symbol of (4(2)·6(3)·8)(4(2)·6). Multicolor luminescence can be tailored from red to green regions by singly varying the mixing molar ratio of Eu(III)/Tb(III) cations. The mixing component of 1Eu/2Tb = 4:6 not only achieves white-light emission with the CIE coordinate of (0.323, 0.339) upon excitation at 405 nm but also presents a temperature recognition property with the significantly high sensitivity of 0.68% per K in the 50-225 K temperature range upon excitation at 370 nm.

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.

PubMed

Kawaguchi, Risa; Kiryu, Hisanori

2016-05-06

RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Our novel software, "ParasoR", is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre

Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey.

PubMed

Tagliani, Elisa; Hassan, Mohamed Osman; Waberi, Yacine; De Filippo, Maria Rosaria; Falzon, Dennis; Dean, Anna; Zignol, Matteo; Supply, Philip; Abdoulkader, Mohamed Ali; Hassangue, Hawa; Cirillo, Daniela Maria

2017-12-15

Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.

Producing genome structure populations with the dynamic and automated PGS software.

PubMed

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

[Human resource capacity building on TB laboratory work for TB control program--through the experience of international TB laboratory training course for TB control at the Research Institute of Tuberculosis, JATA, Japan].

PubMed

Fujiki, Akiko; Kato, Seiya

2008-06-01

The international training course on TB laboratory work for national tuberculosis program (NTP) has been conducted at the Research Institute of Tuberculosis since 1975 funded by Japan International Cooperation Agency in collaboration with WHO Western Pacific Regional Office. The aim of the course is to train key personnel in TB laboratory field for NTP in resource-limited countries. The course has trained 265 national key personnel in TB laboratory service from 57 resource-limited countries in the last 33 years. The number of participants trained may sound too small in the fight against the large TB problem in resource-limited countries. However, every participant is playing an important role as a core and catalyst for the TB control program in his/her own country when they were back home. The curriculum is composed of technical aspects on TB examination, mainly sputum microscopy in addition since microscopy service is provided at many centers that are deployed in a widely spread area, the managerial aspect of maintaining quality TB laboratory work at the field laboratory is another component of the curriculum. Effective teaching methods using materials such as artificial sputum, which is useful for panel slide preparation, and technical manuals with illustrations and pictures of training procedure have been developed through the experience of the course. These manuals are highly appreciated and widely used by the front line TB workers. The course has also contributed to the expansion of EQA (External Quality Assessment) system on AFB microscopy for the improvement of the quality of TB laboratory service of NTP. The course is well-known for not only having a long history, but also for its unique learning method emphasizing "Participatory Training", particularly for practicum sessions to master the skills on AFB microscopy. The method in learning AFB microscopy, which was developed by the course, was published as a training manual by IUATLD, RIT and USAID. As it is

Pathgroups, a dynamic data structure for genome reconstruction problems.

PubMed

Zheng, Chunfang

2010-07-01

Ancestral gene order reconstruction problems, including the median problem, quartet construction, small phylogeny, guided genome halving and genome aliquoting, are NP hard. Available heuristics dedicated to each of these problems are computationally costly for even small instances. We present a data structure enabling rapid heuristic solution to all these ancestral genome reconstruction problems. A generic greedy algorithm with look-ahead based on an automatically generated priority system suffices for all the problems using this data structure. The efficiency of the algorithm is due to fast updating of the structure during run time and to the simplicity of the priority scheme. We illustrate with the first rapid algorithm for quartet construction and apply this to a set of yeast genomes to corroborate a recent gene sequence-based phylogeny. http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html chunfang313@gmail.com Supplementary data are available at Bioinformatics online.

TB Is Back.

ERIC Educational Resources Information Center

Natale, Jo Anna

1992-01-01

The reemergence of tuberculosis, particularly of new drug-resistant strains, points up the need for well-coordinated school health programs. Immigration effects, growing populations of HIV-infected persons, and relaxed screening procedures are partly responsible for TB's reemergence. Two sidebars offer advice on coping with TB at school and…

Ab - initio study of rare earth magnesium alloy: TbMg

NASA Astrophysics Data System (ADS)

Kumari, Meena; Yadav, Priya; Nautiyal, Shashank; Verma, U. P.

2018-05-01

The structural, electronic and magnetic properties of TbMg were analyzed by using full-potential linearized augmented plane wave method. This intermetallic is stable in structure CsCl (B2 phase) with space group Pm-3m. In electronic properties, we show the electronic band structure and density of states plots. These plots show that this alloy have metallic character because there is no band gap between the valance band and conduction band at Fermi level. The structural properties, i.e. equilibrium lattice constant, bulk modulus and its pressure derivative, energy and volume show good agreement with available data. In this paper, we also present the total magnetic moment along with the magnetic moment on the atomic and interstitial sites of TbMg intermetallic in B2 phase.

Evolutionary genomics and population structure of Entamoeba histolytica

PubMed Central

Das, Koushik; Ganguly, Sandipan

2014-01-01

Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba. PMID:25505504

Measurement and analysis of electronic energy transfer between Tb 3+ and Eu 3+ ions in Cs 2NaY 1-x-y Tb xEu yCl 6

NASA Astrophysics Data System (ADS)

Moran, Diane M.; May, P. Stanley; Richardson, F. S.

1994-08-01

Electronic energy-transfer processes between Tb 3+5D 4) and Eu 3+ ( 7F 0, 7F 1) ions in crystalline Cs 2NaY 1-x-yTb xEu yCl 6 compounds are examined over a wide range of relative Tb 3+ and Eu 3+ concentrations (at sample temperature of 77 and 295 K). In these systems, the Tb 3+ and Eu 3+ ions are located at centrosymmetric (O h) sites surrounded by six Cl - ions, and the minimum distance between these sites is ≈ 7.6 Å. The host lattice has a cubic structure (space group O h5-Fm3m), and the phonon spectrum of this lattice has a cut-off frequency of ≈ 300 cm -1. The optical spectra of Tb 3+ and Eu 3+ in Cs 2NaYCl 6 exhibit relatively sparse line structures, consisting almost entirely of magnetic-dipole origin lines and one-phonon-assisted electric-dipole vibronic lines that reflect O h selection rules and have relatively low oscillator strenghts. Overlap between Tb 3+ ( 5D 4) emission and Eu 3+ ( 7F 0, 7F 1) absorption spectra occurs only within the Tb 3+ ( 5D 4 → 7 F 4 and Eu 3+ ( 7F 0, 7F 1 → 5D 0 transition regions, and resonances between individual lines in these regions are used to identify possible pathways for Tb 3+ ( 5D 4)-to-Eu 3+ ( 7F 0, 7F 1) energy transfer. Rates of energy transfer are determined from time-resolved Tb 3+ ( 5D 4) luminescence intersity measurements, analyzed in terms of two different models for representing donor (Tb 3+)-acceptor (Eu 3+) site distributions in Cs 2NaY 1-x-yTb xEu yCl 6 systems. In one model, donor-accepator site distances are represented by a continuous radial distribution function, whereas in the second model, these distances are represented by a discrete distribution function. Both models are used to analyze donor luminescence decay data in terms of rate parameters that reflect specific mechanistic contributions to electronic energy transfer. Both electron-exchange and multipole-multipole mechanisms are considered in the analyses. Results from these analyses, combined with spectral overlap considerations and

Structural, electronic and optical properties of LiNbO3 using GGA-PBE and TB-mBJ functionals: A DFT study

NASA Astrophysics Data System (ADS)

Arshad Javid, M.; Khan, Zafar Ullah; Mehmood, Zahid; Nabi, Azeem; Hussain, Fayyaz; Imran, M.; Nadeem, Muhammad; Anjum, Naeem

2018-06-01

In the present work, first-principles calculations were performed to obtain the structural, electronic and optical properties of lithium niobate crystal using two exchange-correlation functionals (GGA-PBE and TB-mBJ). The calculated structural parameters were very close to the experimental values. TB-mBJ functional was found to be good when compared to LDA and GGA functionals in case of bandgap energy of 3.715 eV of lithium niobate. It was observed that the upper valence and lower conduction bands consist mainly the O-2p and Nb-4d states, respectively. Furthermore, calculations for real and imaginary parts of frequency-dependent dielectric function 𝜀(ω) of lithium niobate crystal were performed using TD-DFT method. The ordinary refractive index no(ω), extraordinary refractive index ne(ω), its birefringence and absorption peaks in imaginary dielectric function 𝜀2(ω) were also calculated.

Child Development and Structural Variation in the Human Genome

ERIC Educational Resources Information Center

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

PubMed Central

Hamilton, Eileen P; Kapusta, Aurélie; Huvos, Piroska E; Bidwell, Shelby L; Zafar, Nikhat; Tang, Haibao; Hadjithomas, Michalis; Krishnakumar, Vivek; Badger, Jonathan H; Caler, Elisabet V; Russ, Carsten; Zeng, Qiandong; Fan, Lin; Levin, Joshua Z; Shea, Terrance; Young, Sarah K; Hegarty, Ryan; Daza, Riza; Gujja, Sharvari; Wortman, Jennifer R; Birren, Bruce W; Nusbaum, Chad; Thomas, Jainy; Carey, Clayton M; Pritham, Ellen J; Feschotte, Cédric; Noto, Tomoko; Mochizuki, Kazufumi; Papazyan, Romeo; Taverna, Sean D; Dear, Paul H; Cassidy-Hanley, Donna M; Xiong, Jie; Miao, Wei; Orias, Eduardo; Coyne, Robert S

2016-01-01

The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena’s germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum. DOI: http://dx.doi.org/10.7554/eLife.19090.001 PMID:27892853

Prognostic score to predict mortality during TB treatment in TB/HIV co-infected patients.

PubMed

Nguyen, Duc T; Jenkins, Helen E; Graviss, Edward A

2018-01-01

Estimating mortality risk during TB treatment in HIV co-infected patients is challenging for health professionals, especially in a low TB prevalence population, due to the lack of a standardized prognostic system. The current study aimed to develop and validate a simple mortality prognostic scoring system for TB/HIV co-infected patients. Using data from the CDC's Tuberculosis Genotyping Information Management System of TB patients in Texas reported from 01/2010 through 12/2016, age ≥15 years, HIV(+), and outcome being "completed" or "died", we developed and internally validated a mortality prognostic score using multiple logistic regression. Model discrimination was determined by the area under the receiver operating characteristic (ROC) curve (AUC). The model's good calibration was determined by a non-significant Hosmer-Lemeshow's goodness of fit test. Among the 450 patients included in the analysis, 57 (12.7%) died during TB treatment. The final prognostic score used six characteristics (age, residence in long-term care facility, meningeal TB, chest x-ray, culture positive, and culture not converted/unknown), which are routinely collected by TB programs. Prognostic scores were categorized into three groups that predicted mortality: low-risk (<20 points), medium-risk (20-25 points) and high-risk (>25 points). The model had good discrimination and calibration (AUC = 0.82; 0.80 in bootstrap validation), and a non-significant Hosmer-Lemeshow test p = 0.71. Our simple validated mortality prognostic scoring system can be a practical tool for health professionals in identifying TB/HIV co-infected patients with high mortality risk.

The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery.

PubMed

Bradley, Anthony R; Echalier, Aude; Fairhead, Michael; Strain-Damerell, Claire; Brennan, Paul; Bullock, Alex N; Burgess-Brown, Nicola A; Carpenter, Elisabeth P; Gileadi, Opher; Marsden, Brian D; Lee, Wen Hwa; Yue, Wyatt; Bountra, Chas; von Delft, Frank

2017-11-08

The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets. © 2017 The

Comparison of the Sensitivity of QuantiFERON-TB Gold In-Tube and T-SPOT.TB According to Patient Age.

PubMed

Bae, Won; Park, Kyoung Un; Song, Eun Young; Kim, Se Joong; Lee, Yeon Joo; Park, Jong Sun; Cho, Young-Jae; Yoon, Ho Il; Yim, Jae-Joon; Lee, Choon-Taek; Lee, Jae Ho

2016-01-01

Currently, there are two types of interferon-gamma release assays (IGRAs) in use for the detection of tuberculosis (TB) infection, the QuantiFERON-TB Gold In-Tube test (GFT-GIT) and T-SPOT.TB. Owing to contradictory reports regarding whether the results of these IGRAs are affected by the age of the patient, we aimed to determine if these two tests have age-related differences in sensitivity. We retrospectively reviewed the medical records of diagnosed TB patients who were tested using either QFT-GIT or T-SPOT.TB from February 2008 to December 2013. The positivity of the two tests was analyzed and compared with true TB infection, which was defined as active TB based on either a positive Mycobacterium culture or a positive TB polymerase chain reaction. The QFT-GIT group included 192 TB patients, and the T-SPOT.TB group included 212 TB patients. Of the patients with pulmonary TB, 76 (39.6%) were in the QFT-GIT group and 143 (67.5%) in the T-SPOT.TB group. The overall sensitivity was 80.2% for QFT-GIT and 91.0% for T.SPOT.TB. The sensitivities of QFT-GIT and T-SPOT.TB according to age group were as follows: <29 years, 93.3% and 96.7%; 30-49 years, 86.5% and 94.7%; 50-69 years, 76.8% and 87.5%; and >70 years, 68.3% and 85.7%, respectively. The trend of age-related changes in sensitivity was significant for both QFT-GIT (p = 0.004) and T.SPOT.TB (p = 0.039). However, only QFT-GIT was significantly related to age in the multivariate analysis. QFT-GIT, but not T-SPOT.TB, was significantly affected by patient age.

Spanning the genomics era: the vital role of a single institution biorepository for childhood cancer research over a decade

PubMed Central

Zhou, Li

2015-01-01

The ‘genomics era’ is considered to have begun with the commencement of the Human Genome Project. As translational genomic studies can only be established when human tissue samples are available for analysis, biospecimens are now proven to be an essential element for their success. During the genomics era the necessity for more extensive biobanking infrastructure has been highlighted. With the increased number of genomic studies into cancer, it is considered that the availability of biospecimens will become the rate limiting step. Despite the efforts in international biobanking, translational genomics is hampered when there low numbers of biospecimens for a particular rare diseases and is most apparent for paediatric cancer. As there is a call for biobanking practice to be responsive to the current experimental needs of the time and for more expansive systems of tissue procurement to be established we have asked the question what role does a single institution biorepository play in the current highly networked world of translational genomics. Here we describe such a case. The Tumour Bank at The Children’s Hospital at Westmead (TB-CHW) in the western suburbs of Sydney was formally established in 1998 as a key resource for translational paediatric cancer research. During the genomics era, we show that the TB-CHW has developed into a key biospecimen repository for the cancer research community, during which time it has increasingly found itself having a vital role in the establishment of translational genomics for paediatric cancer. Here we detail metrics that demonstrate how as a single institution biorepository, the TB-CHW has been a strong participant in the advancement of translational genomics throughout the genomics era. This paper describes the significant contribution of a single institutional hospital embedded tumour biobank to the genomic research community. Despite the increased stringencies placed on biobanking practice, the TB-CHW has shown that a

Structural Genomics and Drug Discovery for Infectious Diseases

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

Anderson, W.F.

The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging,more » or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.« less

Epidemiology of HIV-TB in Asia.

PubMed

Narain, Jai P; Lo, Ying-Ru

2004-10-01

Tuberculosis (TB) has, for centuries, continued to remain a public health problem of enormous importance, particularly in the developing world, taking a heavy toll of those at their prime of life. The emergence of human immunodeficiency virus (HIV infection) and its close association with TB poses an even greater challenge to the health systems in general and TB programmes in particular, in African and Asian countries. HIV is considered to be the most potent risk factor for progression to active TB among those infected both with TB and HIV; as a result, TB is the most common life threatening opportunistic infection associated with HIV, and biggest cause of death among patients with acquired immunodeficiency syndrome (AIDS). In areas hard-hit by HIV, TB is increasing, leading to greater case load, thereby overstretching the already fragile health infrastructure. The deadly relationship between HIV and TB, each potentiating the effect of the other, requires a clearly defined strategy taking into consideration the natural history of the co-infection and its progression to clinical TB (and AIDS). It is clear that the only way to fight this is by bringing the two programmes to join forces and work creatively and innovatively. The strategy should include not only preventing HIV through community-based behavioural interventions and limiting progression to clinical TB through the use of isoniazid preventive therapy, but also early diagnosis and treatment of HIV-associated TB and AIDS using DOTS strategy and combination antiretroviral therapy respectively. The strategy probably would not succeed unless both the programmes are first strengthened before attempting to forge collaboration based on mutual strengths and comparative advantages. In addition, mobilizing national and international response, building partnerships and mobilizing resources will help a great deal in mounting an appropriate and effective response to HIV/TB in the Asian context.

[USE OF QuantiFERON-TB Gold in Tube AND T-SPOT.TB FOR DIAGNOSING PATIENTS WITH SUSPECTED PULMONARY TUBERCULOSIS].

PubMed

Okimoto, Niro; Kurihara, Takeyuki; Miyashita, Naoyuki

2016-04-01

We analyzed the use of QFT-TB Gold in Tube and T-SPOT.TB in diagnosing patients with suspected pulmonary tuberculosis. We evaluated 122 patients with suspected pulmonary tuberculosis (where chest X-ray showed consolidation or. tumor shadow in predilection sites of pulmonary tuberculosis and through contact investigation). QFT-TB Gold and T-SPOT.TB were performed for all the patients. The positive response rate and history of pulmonary tuberculosis in patients who showed positive results for the tests were evaluated. Ninteen patients showed positive results for QFT-TB Gold, and 9, for T-SPOT.TB. Four patients showed positive results for QFT-TB Gold, and 3, for T-SPOT.TB in 4 patients with active tuberculosis. The patients without active tuberculosis whose IGRAs were positive (old pulmonary tuberculosis, Mycobacterium avium cmplex, pneumonia, lung cancer, pulmonary sequestration, bronchiectasis) had a past history of pulmonary tuberculosis. The positive result rate of QFT?-TB Gold was higher than that of T-SPOT.TB in the subjects with suspected pulmonary tuberculosis. We think that QFT-TB Gold reflected the past history of pulmonary tuberculosis.

Extensively Drug-resistant Tuberculosis (XDR-TB): A daunting challenge to the current End TB Strategy and policy recommendations.

PubMed

Rahman, Md Arifur; Sarkar, Atanu

2017-07-01

Extensively Drug-resistant Tuberculosis (XDR-TB) has emerged as one of the most formidable challenges to the End TB Strategy that has targeted a 95% reduction in TB deaths and 90% reduction in cases by 2035. Globally, there were an estimated 55,100 new XDR-TB cases in 2015 in 117 countries. However, only one in 30 XDR-TB cases had been reported so far. Drug susceptibility test (DST) is the mainstay for diagnosing XDR-TB, but the lack of laboratory facilities in the resource-limited endemic countries limit its uses. A few new drugs including bedaquiline and delamanid, have the potential to improve the efficiency of XDR-TB treatment, but the drugs have been included in 39 countries only. The costs of XDR-TB treatment are several folds higher than that of the MDR-TB. Despite the financing from the donors, there is an urgent need to fill the current funding gap of US$ 2 billion to ensure effective treatment and robust surveillance. In the review article we have addressed current update on XDR-TB, including surveillance, diagnosis and the interventions needed to treat and limit its spread, emphasis on extensive financial support for implementing of current recommendations to meet the goals of End TB Strategy. Copyright © 2017 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

Structure and variation of the mitochondrial genome of fishes.

PubMed

Satoh, Takashi P; Miya, Masaki; Mabuchi, Kohji; Nishida, Mutsumi

2016-09-07

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for

Highly aqueous soluble CaF2:Ce/Tb nanocrystals: effect of surface functionalization on structural, optical band gap, and photoluminescence properties.

PubMed

Ansari, Anees A; Parchur, Abdul K; Kumar, Brijesh; Rai, S B

2016-12-01

The design of nanostructured materials with highly stable water-dispersion and luminescence efficiency is an important concern in nanotechnology and nanomedicine. In this paper, we described the synthesis and distinct surface modification on the morphological structure and optical (optical absorption, band gap energy, excitation, emission, decay time, etc.) properties of highly crystalline water-dispersible CaF 2 :Ce/Tb nanocrystals (core-nanocrystals). The epitaxial growth of inert CaF 2 and silica shell, respectively, on their surface forming as CaF 2 :Ce/Tb@CaF 2 (core/shell) and CaF 2 :Ce/Tb@CaF 2 @SiO 2 (core/shell/SiO 2 ) nanoarchitecture. X-ray diffraction and transmission electron microscope image shows that the nanocrystals were in irregular spherical phase, highly crystalline (~20 nm) with narrow size distribution. The core/shell nanocrystals confirm that the surface coating is responsible in the change of symmetrical nanostructure, which was determined from the band gap energy and luminescent properties. It was found that an inert inorganic shell formation effectively enhances the luminescence efficiency and silica shell makes the nanocrystals highly water-dispersible. In addition, Ce 3+ /Tb 3+ -co-doped CaF 2 nanocrystals show efficient energy transfer from Ce 3+ to Tb 3+ ion and strong green luminescence of Tb 3+ ion at 541 nm( 5 D 4 → 7 F 5 ). Luminescence decay curves of core and core/shell nanocrystals were fitted using mono and biexponential equations, and R 2 regression coefficient criteria were used to discriminate the goodness of the fitted model. The lifetime values for the core/shell nanocrystals are higher than core-nanocrystals. Considering the high stable water-dispersion and intensive luminescence emission in the visible region, these luminescent core/shell nanocrystals could be potential candidates for luminescent bio-imaging, optical bio-probe, displays, staining, and multianalyte optical sensing. A newly designed CaF 2 :Ce/Tb

Influence of annealing temperature on structural and optical properties of Lu{sub 2}O{sub 3}:Eu{sup 3+}, Tb{sup 3+} transparent films

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

Morales-Ramírez, Ángel de Jesús; García-Murillo, Antonieta, E-mail: angarciam@ipn.mx; Carrillo-Romo, Felipe de Jesús

2015-10-15

Highlights: • Lu{sub 2}O{sub 3}:Eu{sup 3+}, Tb{sup 3+} films were synthesized by sol–gel and by dip-coating technique. • Effects of annealing treatment on structural and optical properties were studied. • Optogeometrical characteristics of synthesized films were analyzed. • X-ray diffraction results showed that Lu{sub 2}O{sub 3}:Eu{sup 3+}, Tb{sup 3+} crystallizes at 700 °C. • High reddish emission on transparent films with at least 1 μm thick was observed. - Abstract: High-optical quality Lu{sub 2}O{sub 3}:Eu{sup 3+} 5 mol%, X Tb{sup 3+} (X = 0–0.04 mol%) thin films were prepared by the sol–gel process and dip-coating technique. The procedure was asmore » follows: lutetium, europium and terbium nitrates were used as precursors, and ethanol as a solvent. Etylenglycol (EG) was added as a sol stabilizer, and the pH was adjusted by acetic acid. After 10 dipping-cycles, followed by an annealing process (600–900 °C) for 1 h, transparent, smooth and crack-free films (ra = 8–9 nm) were formed. The X-ray diffraction (XRD) results showed crystallized films into the cubic structure at 800 °C. The ellipsometry results showed that the thickness of the films varied from 1 to 1.4 μm at 1000 and 600 °C, respectively. Finally, the films presented a typical Eu{sup 3+} red emission at 611 nm ({sup 5}D{sub 0} → {sup 7}F{sub 2}); furthermore, the effect of the Tb{sup 3+} content showed that the highest emission intensity corresponded to the lower Tb{sup 3+} content.« less

When students become patients: TB disease among medical undergraduates in Cape Town, South Africa.

PubMed

Van der Westhuizen, Helene-Mari; Dramowski, Angela

2017-05-24

Medical students acquire latent tuberculosis (TB) infection at a rate of 23 cases/100 person-years. The frequency and impact of occupational TB disease in this population are unknown. A self-administered questionnaire was distributed via email and social media to current medical students and recently graduated doctors (2010 - 2015) at two medical schools in Cape Town. Individuals who had developed TB disease as undergraduate students were eligible to participate. Quantitative and qualitative data collected from the questionnaire and semi-structured interviews were analysed with descriptive statistics and a framework approach to identify emerging themes. Twelve individuals (10 female) reported a diagnosis of TB: pulmonary TB (n=6), pleural TB (n=3), TB lymphadenitis (n=2) and TB spine (n=1); 2/12 (17%) had drug-resistant disease (DR-TB). Mean diagnostic delay post consultation was 8.1 weeks, with only 42% of initial diagnoses being correct. Most consulted private healthcare providers (general practitioners (n=7); pulmonologists (n=4)), and nine underwent invasive procedures (bronchoscopy, pleural fluid aspiration and tissue biopsy). Substantial healthcare costs were incurred (mean ZAR25 000 for drug-sensitive TB, up to  ZAR104 000 for DR-TB). Students struggled to obtain treatment, incurred high transport costs and missed academic time. Students with DR-TB interrupted their studies and experienced severe side-effects (hepatotoxicity, depression and permanent ototoxicity). Most participants cited poor TB infection-control practices at their training hospitals as a major risk factor for occupational TB. Undergraduate medical students in Cape Town are at high risk of occupationally acquired TB, with an unmet need for comprehensive occupational health services and support.

Detention of People Lost to Follow-Up on TB Treatment in Kenya

PubMed Central

Restoy, Enrique; Kibuchi, Evaline; Holland, Paula; Harries, Anthony D.

2016-01-01

Abstract Adherence to treatment is a key element for global TB control. Public health laws can be used to enforce isolation, adherence, and completion of TB treatment. However, the practical application of public health laws can potentially range from voluntary measures to involuntary detention approaches. This paper explores the potential risks and impacts of using detention approaches to enforce TB treatment adherence. In August 2015, we conducted a literature search regarding the application of public health laws to enforce adherence to TB treatment globally, and specifically in Kenya. Texts were analyzed using narrative synthesis. Results indicated that in Kenya, people lost to follow-up on TB treatment were frequently detained in prisons. However, incarceration and detention approaches curtail the rights to health, informed consent, privacy, freedom from non-consensual treatment, freedom from inhumane and degrading treatment, and freedom of movement of people lost to follow-up. Detention could also worsen social inequalities and lead to a paradoxical increase in TB incidence. We suggest the incorporation of less intrusive solutions in legislation and policies. These include strengthening health systems to reduce dependency on prisons as isolation spaces, decentralizing TB treatment to communities, enhancing treatment education, revising the public health laws, and addressing socioeconomic and structural determinants associated with TB incidence and loss to follow-up. PMID:27780998

TB in Children in the United States

MedlinePlus

... Search Form Controls Cancel Submit Search The CDC Tuberculosis (TB) Note: Javascript is disabled or is not ... message, please visit this page: About CDC.gov . Tuberculosis Basic TB Facts How TB Spreads Latent TB ...

TB control: challenges and opportunities for India.

PubMed

Pai, Madhukar; Daftary, Amrita; Satyanarayana, Srinath

2016-03-01

India's TB control programme has treated over 19 million patients, but the incidence of TB continues to be high. TB is a major killer and drug-resistant TB is a growing threat. There are several likely reasons, including social conditions and co-morbidities that fuel the TB epidemic: under-investment by the government, weak programme implementation and management, suboptimal quality of care in the private sector, and insufficient advocacy around TB. Fortunately, India possesses the technical know-how, competence and resources to address these challenges. The End TB Strategy by WHO offers India an excellent blueprint to advance the agenda of TB control. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Understanding social context on TB cases

NASA Astrophysics Data System (ADS)

Ariyanto, Y.; Wati, D. M.

2017-01-01

Tuberculosis (TB) nowadays still becomes one of the world’s deadliest communicable disease. More than half were in South-East Asia and Western Pacific Regions, including Indonesia. As developing country, Indonesia remains classic problems in overcoming TB, that is discontinuation on treatment. Most of discontinuation on treatment among TB patients are affected by diagnostic delay that caused by patient delay. These phenomena occur in many areas, rural to suburb, coastal to plantation, and so on, and they are related with social context among community that could be social capital for each community to deal with TB. Jember as one of county in East Java is known as plantation area. It also has a high prevalence of TB. This study focused on understanding about social context among community, especially on plantation area. This cross-sectional study involved in three districts of Jember, those are Tanggul, Pakusari, and Kalisat. The data were obtained directly from the TB patients, local community, and Primary Health Care (PHC) where the patients recorded. Spatial analysis and social network analysis (SNA) were applied to obtain health seeking behavior pattern among the TB patients coincide the community. Most of TB patients had already chosen health professionals to lead the treatment, although some of them remained to choose self-medication. Meanwhile, SNA showed that religious leader was considered as main part of countermeasures of TB. But they didn’t ever become central figures. So it can be concluded that there are other parts among community who can contribute due to combatting on TB.

Risk factors for false-negative T-SPOT.TB assay results in patients with pulmonary and extra-pulmonary TB.

PubMed

Pan, Liping; Jia, Hongyan; Liu, Fei; Sun, Huishan; Gao, Mengqiu; Du, Fengjiao; Xing, Aiying; Du, Boping; Sun, Qi; Wei, Rongrong; Gu, Shuxiang; Zhang, Zongde

2015-04-01

To investigate the risk factors for false-negative T-SPOT.TB results in patients with pulmonary TB (PTB) and extra-pulmonary TB (EPTB). Patients with suspected TB who underwent valid T-SPOT.TB tests were prospectively enrolled at Beijing Chest Hospital between November 2012 and November 2013. Basic characters and clinical laboratory findings were compared between true-positive and false-negative T-SPOT.TB groups. Of 1928 suspected TB patients, 774 (530 PTB and 244 EPTB) microbiologically/histopathogenically-confirmed patients (636 culture-confirmed) were analyzed. Forty-six PTB patients (8.7%) and 32 EPTB patients (13.1%) had negative T-SPOT.TB results. Multivariate analysis showed that increased age [odds radio (OR) 2.26, 95% confidence interval (CI) 1.11-4.58], over-weight (BMI ≥ 25 kg/m(2), OR 2.43, 95% CI 1.05-5.63), and a longer period of illness before hospitalization (>6 months, OR 2.46, 95% CI 1.24-4.92) were independent risk factors for false-negative T-SPOT.TB results in PTB patients. In EPTB patients, increased age (OR 2.42, 95% CI 1.09-5.35) also showed an independent association with false-negative T-SPOT.TB results. Careful interpretation of negative T-SPOT.TB results is necessary in older patients with suspected PTB or EPTB, and in PTB patients who are over-weight or have had longer periods of illness before hospitalization. Copyright © 2015 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Perpendicular exchange coupling effects in ferrimagnetic TbFeCo/GdFeCo hard/soft structures

NASA Astrophysics Data System (ADS)

Wang, Ke; Wang, Yahong; Ling, Fujin; Xu, Zhan

2018-04-01

Bilayers consisting of magnetically hard TbFeCo and soft GdFeCo alloy were fabricated. Exchange-spring and sharp switching in a step-by-step fashion were observed in the TbFeCo/GdFeCo hard/soft bilayers with increasing GdFeCo thickness. A perpendicular exchange bias field of several hundred Oersteds is observed from the shift of minor loops pinned by TbFeCo layer. The perpendicular exchange energy is derived to be in the range of 0.18-0.30 erg/cm2. The exchange energy is shown to increase with the thickness of GdFeCo layer in the bilayers, which can be attributed to the enhanced perpendicular anisotropy of GdFeCo layer in our experimental range.

Effect of pH value on structural and photoluminescence properties of Tb3+ -doped Lu2O3 nanopowders synthesized by sol-gel route

NASA Astrophysics Data System (ADS)

Mendoud, A.; Guerbous, L.; Boukerika, A.; Boudine, B.; Benrekaa, N.

2018-01-01

Tb3+-doped Lu2O3 nanophosphors were prepared via simple sol-gel method, at different pH value of solution (2, 5, 8 and 11), using diethanolamine (DEA) as polymerization agent. The nanopowder samples were characterized by X-ray diffraction (XRD), field emission-scanning electron microscopy (FE-SEM), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, room temperature steady and time resolved photoluminescence spectroscopy. The structural analysis reveals that all samples mainely crystallized in the cubic bixbyite structure with Ia3 space group. Also, it was found that the pH value of solution strongly influences the crystallite size, the vibrational frequency modes and the surface morphology of Lu2O3:Tb3+ nanocrystals. All samples show blue-greenish emissions, corresponding to 5D4 → 7FJ (J = 3, 4, 5 and 6) intraconfigurationnelles transitions. The intense green emission peak situated at 542 nm is assigned to 5D4 → 7F5 transition. The 4f8 → 4f75d1 spin-allowed and forbidden transitions, the charge transfer band (CTB) O2- → Tb3+ and the host absorption bands were observed and their dependence on pH value is discussed.

TB tracer teams in South Africa: knowledge, practices and challenges of tracing TB patients to improve adherence.

PubMed

Bristow, Claire C; Podewils, Laura Jean; Bronner, Liza Ellen; Bantubani, Nonkqubela; Walt, Martie van der; Peters, Annatjie; Mametja, David

2013-09-04

In 2008-2009 the South African National Tuberculosis (TB) Program (NTP) implemented a national pilot project, the TB Tracer Project, aiming to decrease default rates and improve patient outcomes. The current study aimed to inform the NTP by describing the knowledge, attitudes, and practices of TB program personnel involved with tracing activities. A self-administered written questionnaire was sent to TB staff, managers and tracer team leaders to assess basic TB knowledge, attitudes and practices. Descriptive statistics were used to summarize results and the chi-squared statistic was used to compare responses of staff at facilities that participated in the TB Tracer Project (tracer) and those that followed standard NTP care (non-tracer). Of 560 total questionnaires distributed, 270 were completed and returned (response rate 48%). Total TB knowledge ranged from 70.8-86.3% correct across all response groups. However, just over half (range 50-59.3%) of each respondent group was able to correctly identify the four components of a DOT encounter. A patient no longer feeling sick was cited by 72.1% of respondents as the reason patients fail to adhere to treatment. Tracer teams were viewed as an effective means to get patients to return to treatment by 96.3% of health facility level respondents. Tracer team leaders reported concerns including lack of logistical support (41.7%), insufficient physical safety precautions (41.7%), and inadequate protection from contracting TB (39.1%). Upon patients returning to treatment at the clinic, facilities included in the TB Tracer Project were significantly more likely to discuss alternate DOTS arrangements than non-tracer facilities (79.2 vs. 66.4%, p = 0.03). This study identified key components of knowledge, attitudes, and practices regarding TB patient tracing activities in South Africa. Educating patients on the essential need to complete treatment irrespective of clinical symptoms may help improve treatment adherence. Future

TB tracer teams in South Africa: knowledge, practices and challenges of tracing TB patients to improve adherence

PubMed Central

2013-01-01

Background In 2008–2009 the South African National Tuberculosis (TB) Program (NTP) implemented a national pilot project, the TB Tracer Project, aiming to decrease default rates and improve patient outcomes. The current study aimed to inform the NTP by describing the knowledge, attitudes, and practices of TB program personnel involved with tracing activities. Methods A self-administered written questionnaire was sent to TB staff, managers and tracer team leaders to assess basic TB knowledge, attitudes and practices. Descriptive statistics were used to summarize results and the chi-squared statistic was used to compare responses of staff at facilities that participated in the TB Tracer Project (tracer) and those that followed standard NTP care (non-tracer). Results Of 560 total questionnaires distributed, 270 were completed and returned (response rate 48%). Total TB knowledge ranged from 70.8-86.3% correct across all response groups. However, just over half (range 50–59.3%) of each respondent group was able to correctly identify the four components of a DOT encounter. A patient no longer feeling sick was cited by 72.1% of respondents as the reason patients fail to adhere to treatment. Tracer teams were viewed as an effective means to get patients to return to treatment by 96.3% of health facility level respondents. Tracer team leaders reported concerns including lack of logistical support (41.7%), insufficient physical safety precautions (41.7%), and inadequate protection from contracting TB (39.1%). Upon patients returning to treatment at the clinic, facilities included in the TB Tracer Project were significantly more likely to discuss alternate DOTS arrangements than non-tracer facilities (79.2 vs. 66.4%, p = 0.03). Conclusions This study identified key components of knowledge, attitudes, and practices regarding TB patient tracing activities in South Africa. Educating patients on the essential need to complete treatment irrespective of clinical symptoms may

Magnetic properties of the Tb4 + ion in Li2TbF6

NASA Astrophysics Data System (ADS)

Guillot, M.; El-Ghozzi, M.; Avignant, D.; Ferey, G.

1993-05-01

Both oxygen and fluorine have a partiality towards the stabilization of high oxidation states of rare earths such as Ce, Pr, and Tb. During the study of the MF-M'F4 (M=alkaline metal; M' rare ion) the compound Li2TbF6 was found to constitute the only representative obtained under ambient pressure of a structural type, namely α-Li2ZrF6, known until now only through the high pressure form. Magnetic measurements were carried out over the 1.4-300 K temperature range in continuous magnetic fields up to 20 T produced by a Bitter magnet. At low temperature and in H higher than 15 T, the magnetization M was observed to be field independent and very close to the calculated Tb4+ free ion value, i.e., 7μB; on the other hand, the data do not present any departure from the Brillouin function of the pure 8S7/2 state. The reciprocal magnetic susceptibility obeys a Curie-Weiss law leading to an effective moment of 7.86μB. A very unusual behavior of the terbium ion which presents a 4+ oxidation state is concluded: to the best of our knowledge, it is the first observation of this form. The so-found spherical 4f7 electronic configuration is the most compatible with the high coordination number of eight. Finally, the discussion within the series Li2MIVF6 compounds to understand the influence of both electronic configuration and size effects is presented.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Chloroplast genome resources and molecular markers differentiate rubber dandelion species from weedy relatives.

PubMed

Zhang, Yingxiao; Iaffaldano, Brian J; Zhuang, Xiaofeng; Cardina, John; Cornish, Katrina

2017-02-02

Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two weedy dandelion species, Taraxacum brevicorniculatum (TB) and the common dandelion (Taraxacum officinale, TO). TB is often present as a seed contaminant within TK accessions, while TO is a pandemic weed, which may have the potential to hybridize with TK. To discriminate these species at the molecular level, and facilitate gene flow studies between the potential rubber crop, TK, and its weedy relatives, we generated genomic and marker resources for these three dandelion species. Complete chloroplast genome sequences of TK (151,338 bp), TO (151,299 bp), and TB (151,282 bp) were obtained using the Illumina GAII and MiSeq platforms. Chloroplast sequences were analyzed and annotated for all the three species. Phylogenetic analysis within Asteraceae showed that TK has a closer genetic distance to TB than to TO and Taraxacum species were most closely related to lettuce (Lactuca sativa). By sequencing multiple genotypes for each species and testing variants using gel-based methods, four chloroplast Single Nucleotide Polymorphism (SNP) variants were found to be fixed between TK and TO in large populations, and between TB and TO. Additionally, Expressed Sequence Tag (EST) resources developed for TO and TK permitted the identification of five nuclear species-specific SNP markers. The availability of chloroplast genomes of these three dandelion species, as well as chloroplast and nuclear molecular markers, will provide a powerful genetic resource for germplasm differentiation and purification, and the study of potential gene flow among Taraxacum species.

Functional RNA structures throughout the Hepatitis C Virus genome.

PubMed

Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

2017-06-01

The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

HIV screening among TB patients and co-trimoxazole preventive therapy for TB/HIV patients in Addis Ababa: facility based descriptive study.

PubMed

Denegetu, Amenu Wesen; Dolamo, Bethabile Lovely

2014-01-01

Collaborative TB/HIV management is essential to ensure that HIV positive TB patients are identified and treated appropriately, and to prevent tuberculosis (TB) in HIV positive patients. The purpose of this study was to assess HIV case finding among TB patients and Co-trimoxazole Preventive Therapy (CPT) for HIV/TB patients in Addis Ababa. A descriptive cross-sectional, facility-based survey was conducted between June and July 2011. Data was collected by interviewing 834 TB patients from ten health facilities in Addis Ababa. Both descriptive and inferential statistics were used to summarize and analyze findings. The proportion of TB patients who (self reported) were offered for HIV test, tested for HIV and tested HIV positive during their anti-TB treatment follow-up were; 87.4%, 69.4% and 20.2%; respectively. Eighty seven HIV positive patients were identified, who knew their status before diagnosed for the current TB disease, bringing the cumulative prevalence of HIV among TB patients to 24.5%. Hence, the proportion of TB patients who knew their HIV status becomes 79.9%. The study revealed that 43.6% of those newly identified HIV positives during anti-TB treatment follow-up were actually treated with CPT. However, the commutative proportion of HIV positive TB patients who were ever treated with CPT was 54.4%; both those treated before the current TB disease and during anti-TB treatment follow-up. HIV case finding among TB patients and provision of CPT for TB/HIV co-infected patients needs boosting. Hence, routine offering of HIV test and provision of CPT for PLHIV should be strengthened in-line with the national guidelines.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

PubMed

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

Noncollinear spin structure in SmxTb1-x[Cr(CN)6]•4H2O having orthogonal single-ion anisotropies

NASA Astrophysics Data System (ADS)

Hozumi, Toshiya; Hashimoto, Kazuhito; Ohkoshi, Shin-Ichi

2006-03-01

A series of SmxIIITb1-xIII[CrIII(CN)6]•4H2O magnets, in which SmIII and TbIII have different magnetic single-ion anisotropies, was prepared. Magnetic ordering temperatures (Tc) decreased from 12.0K (x=0) to 7.4K (x=0.55) and then increased to 10.2K (x=1) with increasing x . The magnetization (Ms) values at 5K gradually decreased from 3.0μB (x=0) to 1.6μB (x=1) . These trends of experimental Tc and Ms values suggest that the present series takes a noncollinear spin structure, in which the directions of the SmIII and TbIII sublattice magnetizations are perpendicular, from the analysis of the molecular-field model.

Genome expansion and gene loss in powdery mildew fungi reveal functional tradeoffs in extreme parasitism

USDA-ARS?s Scientific Manuscript database

Eukaryotic genomes vary in size over five orders of magnitude ranging from microsporidia (~2.9Mb) to the lung-fish (~1.2Tb). This extraordinary variation is largely a result of the proliferation of mobile DNA elements also referred to as “genomic parasites.” The constraints on genome size may be imp...

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

Potential Function of Granulysin, Other Related Effector Molecules and Lymphocyte Subsets in Patients with TB and HIV/TB Coinfection

PubMed Central

Pitabut, Nada; Sakurada, Shinsaku; Tanaka, Takahiro; Ridruechai, Chutharut; Tanuma, Junko; Aoki, Takahiro; Kantipong, Pacharee; Piyaworawong, Surachai; Kobayashi, Nobuyuki; Dhepakson, Panadda; Yanai, Hideki; Yamada, Norio; Oka, Shinichi; Okada, Masaji; Khusmith, Srisin; Keicho, Naoto

2013-01-01

Background: Host effector mechanism against Mycobacterium tuberculosis (Mtb) infection is dependent on innate immune response by macrophages and neutrophils and the alterations in balanced adaptive immunity. Coordinated release of cytolytic effector molecules from NK cells and effector T cells and the subsequent granule-associated killing of infected cells have been documented; however, their role in clinical tuberculosis (TB) is still controversy. Objective: To investigate whether circulating granulysin and other effector molecules are associated with the number of NK cells, iNKT cells, Vγ9+Vδ2+ T cells, CD4+ T cells and CD8+ T cells, and such association influences the clinical outcome of the disease in patients with pulmonary TB and HIV/TB coinfection. Methods: Circulating granulysin, perforin, granzyme-B and IFN-γ levels were determined by ELISA. The isoforms of granulysin were analyzed by Western blot analysis. The effector cells were analyzed by flow cytometry. Results: Circulating granulysin and perforin levels in TB patients were lower than healthy controls, whereas the granulysin levels in HIV/TB coinfection were much higher than in any other groups, TB and HIV with or without receiving HAART, which corresponded to the number of CD8+ T cells which kept high, but not with NK cells and other possible cellular sources of granulysin. In addition, the 17kDa, 15kDa and 9kDa isoforms of granulysin were recognized in plasma of HIV/TB coinfection. Increased granulysin and decreased IFN-γ levels in HIV/TB coinfection and TB after completion of anti-TB therapy were observed. Conclusion: The results suggested that the alteration of circulating granulysin has potential function in host immune response against TB and HIV/TB coinfection. This is the first demonstration so far of granulysin in HIV/TB coinfection. PMID:23801887

The Use of Functional Genomics in Conjunction with Metabolomics for Mycobacterium tuberculosis Research

PubMed Central

Swanepoel, Conrad C.

2014-01-01

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a fatal infectious disease, resulting in 1.4 million deaths globally per annum. Over the past three decades, genomic studies have been conducted in an attempt to elucidate the functionality of the genome of the pathogen. However, many aspects of this complex genome remain largely unexplored, as approaches like genomics, proteomics, and transcriptomics have failed to characterize them successfully. In turn, metabolomics, which is relatively new to the “omics” revolution, has shown great potential for investigating biological systems or their modifications. Furthermore, when these data are interpreted in combination with previously acquired genomics, proteomics and transcriptomics data, using what is termed a systems biology approach, a more holistic understanding of these systems can be achieved. In this review we discuss how metabolomics has contributed so far to characterizing TB, with emphasis on the resulting improved elucidation of M. tuberculosis in terms of (1) metabolism, (2) growth and replication, (3) pathogenicity, and (4) drug resistance, from the perspective of systems biology. PMID:24771957

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

PubMed Central

Ritchey, Laura E.; Su, Zhao; Tang, Yin; Tack, David C.

2017-01-01

Abstract RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. PMID:28637286

Multidrug-Resistant TB

PubMed Central

Cox, Helen; Coomans, Fons

2016-01-01

Abstract The right to enjoy the benefits of scientific progress (REBSP) is a little-known but potentially valuable right that can contribute to rights-based approaches to addressing multidrug-resistant TB (MDR-TB). We argue that better understanding of the REBSP may help to advance legal and civil society action for health rights. While the REBSP does not provide an individual entitlement to have a new drug developed for MDR-TB, it sets up entitlements to expect a state to establish a legislative and policy framework aimed at developing scientific capacity to address the most important health issues and at disseminating the outcomes of scientific research. By making scientific findings available and accessible, people can be enabled to claim the use of science for social benefits. Inasmuch as the market fails to address neglected diseases such as MDR-TB, the REBSP provides a potential counterbalance to frame a positive obligation on states to both marshal their own resources and to coordinate the actions of multiple other actors towards this goal, including non-state actors. While the latter do not hold the same level of accountability as states, the REBSP can still enable the recognition of obligations at a level of “soft law” responsibilities. PMID:27780997

Coordination ability determined transition metal ions substitution of Tb in Tb-Asp fluorescent nanocrystals and a facile ions-detection approach.

PubMed

Duan, Jiazhi; Ma, Baojin; Liu, Feng; Zhang, Shan; Wang, Shicai; Kong, Ying; Du, Min; Han, Lin; Wang, Jianjun; Sang, Yuanhua; Liu, Hong

2018-04-26

Although the synthesis and fluorescent properties of lanthanide-amino acid complex nanostructures have been investigated extensively, limited studies have been reported on metal ions' substitution ability for the lanthanide ions in the complex and their effect on the fluorescent property. In this study, taking biocompatible Tb-aspartic acid (Tb-Asp) complex nanocrystals as a model, the substitution mechanism of metal ions, particularly transition metals, for Tb ions in Tb-Asp nanocrystals and the change in the fluorescent property of the Tb-Asp nanocrystals after substitution were systematically investigated. The experimental results illustrated that metal ions with higher electronegativity, higher valence, and smaller radius possess stronger ability for Tb ions' substitution in Tb-Asp nanocrystals. Based on the effect of substituting ions' concentration on the fluorescent property of Tb-Asp, a facile method for copper ions detection with high sensitivity was proposed by measuring the fluorescent intensity of Tb-Asp nanocrystals' suspensions containing different concentrations of copper ions. The good biocompatibility, great convenience of synthesis and sensitive detection ability make Tb-Asp nanocrystals a very low cost and effective material for metal ions detection, which also opens a new door for practical applications of metal-Asp coordinated nanocrystals.

TB infection prevention and control experiences of South African nurses - a phenomenological study

PubMed Central

2011-01-01

Background The tuberculosis (TB) epidemic in South Africa is characterised by one of the highest levels of TB/HIV co-infection and growing multidrug-resistant TB worldwide. Hospitals play a central role in the management of TB. We investigated nurses' experiences of factors influencing TB infection prevention and control (IPC) practices to identify risks associated with potential nosocomial transmission. Methods The qualitative study employed a phenomenological approach, using semi-structured interviews with a quota sample of 20 nurses in a large tertiary academic hospital in Cape Town, South Africa. The data was subjected to thematic analysis. Results Nurses expressed concerns about the possible risk of TB transmission to both patients and staff. Factors influencing TB-IPC, and increasing the potential risk of nosocomial transmission, emerged in interconnected overarching themes. Influences related to the healthcare system included suboptimal IPC provision such as the lack of isolation facilities and personal protective equipment, and the lack of a TB-IPC policy. Further influences included inadequate TB training for staff and patients, communication barriers owing to cultural and linguistic differences between staff and patients, the excessive workload of nurses, and a sense of duty of care. Influences related to wider contextual conditions included TB concerns and stigma, and the role of traditional healers. Influences related to patient behaviour included late uptake of hospital care owing to poverty and the use of traditional medicine, and poor adherence to IPC measures by patients, family members and carers. Conclusions Several interconnected influences related to the healthcare system, wider contextual conditions and patient behavior could increase the potential risk of nosocomial TB transmission at hospital level. There is an urgent need for the implementation and evaluation of a comprehensive contextually appropriate TB IPC policy with the setting and

One of the possible mechanisms for the inhibition effect of Tb(III) on peroxidase activity in horseradish (Armoracia rusticana) treated with Tb(III).

PubMed

Guo, Shaofen; Cao, Rui; Lu, Aihua; Zhou, Qing; Lu, Tianhong; Ding, Xiaolan; Li, Chaojun; Huang, Xiaohua

2008-05-01

One of the possible mechanisms for the inhibition effect of Tb(III) on peroxidase activity in horseradish (Armoracia rusticana) treated with Tb(III) was investigated using some biophysical and biochemical methods. Firstly, it was found that a large amount of Tb(III) can be distributed on the cell wall, that some Tb(III) can enter into the horseradish cell, indicating that peroxidase was mainly distributed on cell wall, and thus that Tb(III) would interact with horseradish peroxidase (HRP) in the plant. In addition, peroxidase bioactivity was decreased in the presence of Tb(III). Secondly, a new peroxidase-containing Tb(III) complex (Tb-HRP) was obtained from horseradish after treatment with Tb(III); the molecular mass of Tb-HRP is near 44 kDa and the pI is about 8.80. Thirdly, the electrocatalytic activity of Tb-HRP is much lower than that of HRP obtained from horseradish without treatment with Tb(III). The decrease in the activity of Tb-HRP is due to the destruction (unfolding) of the conformation in Tb-HRP. The planarity of the heme active center in the Tb-HRP molecule was increased and the extent of exposure of Fe(III) in heme was decreased, leading to inhibition of the electron transfer. The microstructure change in Tb-HRP might be the result of the inhibition effect of Tb(III) on peroxidase activity in horseradish.

Magnetism of Ho 1-xTb xAl₂ alloys: Critical dependence of a first-order transition on Tb concentration

DOE PAGES

Khan, Mahmud; Mudryk, Ya.; Gschneidner, K. A.; ...

2011-12-27

HoAl₂ exhibits a first-order spin reorientation transition at 20 K, which is manifested as a sharp peak in the heat capacity. When Ho is partially replaced by only 5% of Tb, the sharp heat-capacity peak in Ho 1-xTb xAl₂ (x = 0.05) disappears, and then reappears again for x ≥ 0.07. For x = 0.05, the anomaly corresponding to the spin reorientation transition is barely seen in the heat capacity, but as x exceeds 0.07 the weak anomaly transforms to a sharp peak. The spin reorientation transition temperature increases to 29 K for x = 0.05, and as x increasesmore » further the transition shifts to lower temperature and returns to ~20 K for x = 0.25. The transition is no longer observed when x exceeds 0.60. Temperature-dependent x-ray powder-diffraction data confirm the first-order nature of the spin reorientation transition for the alloy with x = 0.40, and indicate that the compound retains the room-temperature cubic structure within the sensitivity of the technique. Experimental observations are discussed considering the easy magnetization directions of HoAl₂ and TbAl₂.« less

Structure and luminescence properties of Tb3+-doped Lu3Al5O12 films prepared by Pechini sol-gel method

NASA Astrophysics Data System (ADS)

Wang, Jian; Shen, Siqing; Xie, Jianjun; Shi, Ying; Ai, Fei

2011-02-01

Tb3+-doped Lu3Al5O12(hereinafter referred to as LuAG:Tb) films were successfully prepared by Pechini sol-gel process and spin-coating technique on carefully cleaned (111) silicon wafer. The microstructure and optical properties of the LuAG:Tb films were studied by X-ray diffraction (XRD), atomic force microscopy(AFM), as well as photoluminescence (PL) spectra. The XRD results showed that the precursor films started to crystallize at about 900°C. All as-calcined LuAG:Tb films showed the Tb3+ characteristic emission bands.

Structure and luminescence properties of Tb3+-doped Lu3Al5O12 films prepared by Pechini sol-gel method

NASA Astrophysics Data System (ADS)

Wang, Jian; Shen, Siqing; Xie, Jianjun; Shi, Ying; Ai, Fei

2010-10-01

Tb3+-doped Lu3Al5O12(hereinafter referred to as LuAG:Tb) films were successfully prepared by Pechini sol-gel process and spin-coating technique on carefully cleaned (111) silicon wafer. The microstructure and optical properties of the LuAG:Tb films were studied by X-ray diffraction (XRD), atomic force microscopy(AFM), as well as photoluminescence (PL) spectra. The XRD results showed that the precursor films started to crystallize at about 900°C. All as-calcined LuAG:Tb films showed the Tb3+ characteristic emission bands.

Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB

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

Chen, Wenjing; Biswas, Tapan; Porter, Vanessa R.

2011-09-06

The emergence of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis (TB) is a serious global threat. Aminoglycoside antibiotics are used as a last resort to treat XDR-TB. Resistance to the aminoglycoside kanamycin is a hallmark of XDR-TB. Here, we reveal the function and structure of the mycobacterial protein Eis responsible for resistance to kanamycin in a significant fraction of kanamycin-resistant Mycobacterium tuberculosis clinical isolates. We demonstrate that Eis has an unprecedented ability to acetylate multiple amines of many aminoglycosides. Structural and mutagenesis studies of Eis indicate that its acetylation mechanism is enabled by a complex tripartite fold that includes two generalmore » control non-derepressible 5 (GCN5)-related N-acetyltransferase regions. An intricate negatively charged substrate-binding pocket of Eis is a potential target of new antitubercular drugs expected to overcome aminoglycoside resistance.« less

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

Enhancing TB case detection: experience in offering upfront Xpert MTB/RIF testing to pediatric presumptive TB and DR TB cases for early rapid diagnosis of drug sensitive and drug resistant TB.

PubMed

Raizada, Neeraj; Sachdeva, Kuldeep Singh; Nair, Sreenivas Achuthan; Kulsange, Shubhangi; Gupta, Radhey Shayam; Thakur, Rahul; Parmar, Malik; Gray, Christen; Ramachandran, Ranjani; Vadera, Bhavin; Ekka, Shobha; Dhawan, Shikha; Babre, Ameet; Ghedia, Mayank; Alavadi, Umesh; Dewan, Puneet; Khetrapal, Mini; Khanna, Ashwini; Boehme, Catharina; Paramsivan, Chinnambedu Nainarappan

2014-01-01

Diagnosis of pulmonary tuberculosis (PTB) in children is challenging due to difficulties in obtaining good quality sputum specimens as well as the paucibacillary nature of disease. Globally a large proportion of pediatric tuberculosis (TB) cases are diagnosed based only on clinical findings. Xpert MTB/RIF, a highly sensitive and specific rapid tool, offers a promising solution in addressing these challenges. This study presents the results from pediatric groups taking part in a large demonstration study wherein Xpert MTB/RIF testing replaced smear microscopy for all presumptive PTB cases in public health facilities across India. The study covered a population of 8.8 million across 18 programmatic sub-district level tuberculosis units (TU), with one Xpert MTB/RIF platform established at each study TU. Pediatric presumptive PTB cases (both TB and Drug Resistant TB (DR-TB)) accessing any public health facilities in study area were prospectively enrolled and tested on Xpert MTB/RIF following a standardized diagnostic algorithm. 4,600 pediatric presumptive pulmonary TB cases were enrolled. 590 (12.8%, CI 11.8-13.8) pediatric PTB were diagnosed. Overall 10.4% (CI 9.5-11.2) of presumptive PTB cases had positive results by Xpert MTB/RIF, compared with 4.8% (CI 4.2-5.4) who had smear-positive results. Upfront Xpert MTB/RIF testing of presumptive PTB and presumptive DR-TB cases resulted in diagnosis of 79 and 12 rifampicin resistance cases, respectively. Positive predictive value (PPV) for rifampicin resistance detection was high (98%, CI 90.1-99.9), with no statistically significant variation with respect to past history of treatment. Upfront access to Xpert MTB/RIF testing in pediatric presumptive PTB cases was associated with a two-fold increase in bacteriologically-confirmed PTB, and increased detection of rifampicin-resistant TB cases under routine operational conditions across India. These results suggest that routine Xpert MTB/RIF testing is a promising solution to

Community engagement for paediatric MDR-TB clinical trials: principles to support ethical trial implementation.

PubMed

Hoddinott, G; Staples, S; Brown, R; Simwinga, M; Mubekapi-Musadaidzwa, C; Hesseling, A C; Hendricks, G; De Koker, P; McKenna, L

2018-05-01

The paediatric tuberculosis (TB) prevention and treatment landscape is moving into a new and exciting era, with knowledge from clinical trials offering real benefit to children. Community engagement is key to optimising the success of these trials. However, the clinical profile, epidemiology and social perceptions for paediatric multidrug-resistant TB (MDR-TB) complicate the operationalisation of this community engagement. We reflect on a diversity of recent experiences attempting to implement this type of research and the community engagement around it. We describe four recommendations and argue that these should guide the implementation of the community engagement agenda in the new landscape of paediatric MDR-TB clinical trials. Specifically, we argue for 1) dynamic, long-term continuity in community engagement platforms; 2) tiers of TB and research literacy; 3) multiple separate and joint platforms for holding 'stakes'; and 4) addressing the social/structural implications of family participation. We conclude that community-level stakeholders, such as health workers, parents and children, are willing to collaborate in paediatric MDR-TB clinical trials. Using these recommendations, there is considerable opportunity for effective community engagement in this new era of paediatric MDR-TB research.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

PubMed Central

Peng, Yanhui; Loparev, Vladimir; Batra, Dhwani; Bowden, Katherine E.; Burroughs, Mark; Cassiday, Pamela K.; Davis, Jamie K.; Johnson, Taccara; Juieng, Phalasy; Knipe, Kristen; Mathis, Marsenia H.; Pruitt, Andrea M.; Rowe, Lori; Sheth, Mili; Tondella, M. Lucia; Williams, Margaret M.

2017-01-01

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile

Synthesis and characterization of Mg2SiO4:Tb3+, Eu3+ phosphors for white light generation

NASA Astrophysics Data System (ADS)

Cho, Shinho

2016-09-01

The effect of Eu3+ codoping on the structural, morphological, and optical properties of Mg2SiO4:Tb3+ was investigated. The phosphor powders were synthesized by changing the molar concentration of Eu3+ at a fixed Tb3+ content of 5 mol% by using a conventional solid-state reaction. The X-ray diffraction patterns revealed that the crystal structure of all the phosphors, irrespective of the Eu3+ and the Tb3+ contents, showed an orthorhombic structure, and the surface morphology exhibited pebble-like crystalline grains. The emission spectra of Eu3+ and Tb3+-codoped Mg2SiO4 phosphors under an ultraviolet excitation of 252 nm consisted of one intense red band at 619 nm and five weak bands at 448, 488, 598, 658, and 707 nm originating from the transitions of Eu3+, in addition to the several emission bands located at 492, 552, 592, and 628 nm arising from the transitions of Tb3+. As the Eu3+ content was increased, the intensity of the main green emission band at 552 nm decreased markedly and disappeared at 10 mol% Eu3+, when complete energy transfer from Tb3+ to Eu3+ was observed. The results suggest that the emission wavelength and the luminescent intensity of the phosphors can be tuned by modulating the Eu3+ and the Tb3+ contents incorporated into the host matrix.

HIV and TB co-infection in Indian context.

PubMed

Mahyoub, E M; Garg, Suneela; Singh, M M; Agarwal, Paras; Gupta, V K; Gupta, Naresh

2013-01-01

This study was carried out in a Anti-Retroviral Therapy Clinic and TB center of a tertiary level hospital to find out socio-demographic correlates of HIV/TB individuals and risk factors of HIV/TB co-infection in Indian context. It is a case-control study comprising 420 subjects, 3 groups of 140 each. For a case group of HIV-TB co-infected subjects, two control groups, one comprising HIV patients (not having TB), and the other TB patients (not having HIV). Majority 267 (63.6%) males, 100 (71.4%) in case group (HIV/ TB), 74 (52.9%) in control group 1 (TB) and 93 (66.4%) in control group 2 (HIV). Mean (+/-SD) age of case-group was 34.91 (+/- 8.57) years. New TB cases were 213 (76.1%), more among control-group 1, compared to case-group. Multivariate analysis showed that risk of co-infection was 1.94 times higher among individuals aged >35 years. Difference statistically significant amongst those who were not on ART than who were on ART (p < 0.001). Those with CD4 counts <200 had 1.85 times risk of TB. Smokers had 1.92 times risk of TB. Co-infection higher in males, in age group 35-44 years, urban area, lower educational status and lower socioeconomic class. Current history of smoking significantly associated with co-infection. HIV status during TB infection was detected in 1/4th of study subjects. History of TB symptoms in family significantly associated with co-infection.

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging

PubMed Central

Stewart, H.; Bingham, R.J.; White, S. J.; Dykeman, E. C.; Zothner, C.; Tuplin, A. K.; Stockley, P. G.; Twarock, R.; Harris, M.

2016-01-01

The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly. PMID:26972799

Immune TB Antibody Phage Display Library as a Tool To Study B Cell Immunity in TB Infections.

PubMed

Hamidon, Nurul Hamizah; Suraiya, Siti; Sarmiento, Maria E; Acosta, Armando; Norazmi, Mohd Nor; Lim, Theam Soon

2018-03-01

B cells and in particular antibodies has always played second fiddle to cellular immunity in regard to tuberculosis (TB). However, recent studies has helped position humoral immunity especially antibodies back into the foray in relation to TB immunity. Therefore, the ability to correlate the natural antibody responses of infected individuals toward TB antigens would help strengthen this concept. Phage display is an intriguing approach that can be utilized to study antibody-mediated responses against a particular infection via harvesting the B cell repertoire from infected individuals. The development of disease-specific antibody libraries or immune libraries is useful to better understand antibody-mediated immune responses against specific disease antigens. This study describes the generation of an immune single-chain variable fragment (scFv) library derived from TB-infected individuals. The immune library with an estimated diversity of 10 9 independent clones was then applied for the identification of monoclonal antibodies against Mycobacterium tuberculosis α-crystalline as a model antigen. Biopanning of the library isolated three monoclonal antibodies with unique gene usage. This strengthens the role of antibodies in TB immunity in addition to the role played by cellular immunity. The developed library can be applied against other TB antigens and aid antibody-derived TB immunity studies in the future.

Phase transformations and indications for acoustic mode softening in Tb-Gd orthophosphate

DOE PAGES

Tschauner, Oliver; Ushakov, Sergey V.; Navrotsky, Alexandra; ...

2016-01-06

At ambient conditions the anhydrous rare-earth orthophosphates assume either the xenotime (zircon) or the monazite structure, with the latter favored for the heavier rare earths. Tb 0.5Gd 0.5PO 4 assumes the xenotime structure at ambient conditions but is at the border between the xenotime and monazite structures. Here we show that, at high pressure, Tb 0.5Gd 0.5PO 4 does not transform directly to monazite but through an intermediate anhydrite-type structure. We show softening of (c 1133 + c 1313) combined elastic moduli close to the transition from the anhydrite to the monazite structure. Stress response of rare-earth orthophosphate ceramics canmore » be affected by both formation of the anhydrite-type phase and the elastic softening in the vicinity of the monazite-phase. In conclusion, we report the first structural data for an anhydrite-type rare earth orthophosphate.« less

Controllable synthesis of Ln3+ (Ln = Tb, Eu) doped zinc phosphate nano-/micro-structured materials: phase, morphology and luminescence properties.

PubMed

Yue, Dan; Lu, Wei; Li, Chunyang; Zhang, Xinlei; Liu, Chunxia; Wang, Zhenling

2014-02-21

Ln(3+) (Ln = Tb, Eu) doped zinc phosphate tetrahydrate (ZPT:Ln(3+)) and ammonium zinc phosphate (AZP:Ln(3+)) nano-/micro-structured materials were synthesized in aqueous solution without the addition of any structure-directing agent. The phase structures, morphologies and luminescence properties of the as-synthesized samples were investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), photoluminescence (PL) spectroscopy and lifetime. These investigations indicate that different phosphate sources MnH(3-n)PO4 (M = NH4(+) or Na(+), n = 1, 2, 3) can lead to the altering of morphology from nanosheet to microflower, but have no significant effect on the phase structure of the samples. The microlump, nanosheet, and microflower (constructed by the primary microlumps or nanosheets) of orthorhombic ZPT:Ln(3+) could be selectively prepared by adjusting the pH value from 3.5 to 7.0. A mixture of orthorhombic ZPT:Ln(3+) and monoclinic AZP:Ln(3+) with a microflower morphology was obtained when the pH value was adjusted to 8.0. Monoclinic AZP:Ln(3+) microplate, microcube and nanoparticle morphologies were obtained at pH values of 8.5, 9.0 and 11.0 respectively. The phase transformation and growth mechanism of the diverse morphologies were proposed, and ZPT:Ln(3+) (Ln(3+) = Eu or Tb) samples exhibit red or green emission under the excitation of UV light.

Patent protection for structural genomics-related inventions.

PubMed

Vinarov, Sara D

2003-01-01

Recently there have been some important developments with respect to the patentability of inventions in the field of structural genomics. The leaders of the European Patent Office (EPO), Japan Patent Office (JPO) and the United States Patent Office (USPTO) came together for a trilateral meeting to conduct a comparative study on protein 3-dimensional (3-D) structure related claims in an effort to come to a mutual understanding about the examination of such inventions. The three patent offices were presented with eight different cases: 1) 3-D structural data of a protein per se; 2) computer-readable storage medium encoded with structural data of a protein; 3) protein defined by its tertiary structure; 4) crystals of known proteins; 5) binding pockets and protein domains; 6) and 7) are both directed to in silico screening methods directed to a specific protein; and 8) pharmacophores. The preliminary conclusions reached at the trilateral meeting provide clarity regarding the types of inventions that may be patentable given a specific set of scientific facts in a patent application. Therefore, the guidance provided by this study will help inventors, attorneys and other patent practitioners who file for patent protection on structural genomics-based inventions both here and abroad comply with the patentability requirements of each office.

Investigation of Tb 3+ ion fluorescence properties in γ-irradiated poly(ethylene oxide)-TbCl 3 blended systems

NASA Astrophysics Data System (ADS)

Cho, Myung D.; Okamoto, Yoshiyuki

1995-05-01

Degradation of polymers by γ-irradiation using Tb 3+ ion as a fluorescence probe was investigated. When poly(ethylene oxide) blended with TbCl 3 films were γ-irradiated in air, the fluorescence intensity of Tb 3+ was found to be greatly increased and the molecular weights of PEO were decreased. These results suggest that radiolysis caused chain degradation of PEO and produced carbonyl groups at the end of the cleaved polymer chain. The chromophore moiety produced transfers energy to Tb 3+ ion located within the non-irradiative energy trasfer distance. It is suggested that blended films of PEO with Tb 3+ may be used as convenient and fast detectors of γ-irradiation doses.

Framework of behavioral indicators evaluating TB health promotion outcomes: a modified Delphi study of TB policymakers and health workers.

PubMed

Li, Ying; Ehiri, John; Hu, Daiyu; Oren, Eyal; Cao, Jia

2015-12-15

Although TB health promotion directed at policy makers and healthcare workers (HCWs) is considered important to tuberculosis (TB) control, no indicators currently assess the impact of such promotional activities. This article is the second in a series of papers that seek to establish a framework of behavioral indicators for outcome evaluation of TB health promotion, using the Delphi method. In the first article, we sought to establish a framework of behavioral indicators for outcome evaluation of TB health promotion among TB suspects and patients. The objective of this second article is to present an indicator framework that can be used to assess behavioral outcomes of TB health promotion directed at policy makers and HCWs. A two-round, modified Delphi method was used to establish the indicators. Sixteen experts who were knowledgeable and experienced in the field of TB control were consulted in Delphi surveys. A questionnaire was developed following 4 steps, and involved ranking indicators on a five-point Likert scale. The consensus level was 70 %. Median, mode, and Coefficient of variation (CV) were used to describe expert responses. An authority coefficient (Cr) was used to assess the degree of each expert's authority. Consensus was achieved following the two survey rounds and several iterations among the experts. For TB health-promotion activities directed at policymakers, the experts reached consensus on 2 domains ("Resource inputs" and "Policymaking and monitoring behaviors"), 4 subdomains ("Human resources" among others), and 13 indicators ("Human resources per 100,000 person" among others). For TB health-promotion activities directed at HCWs, the experts reached consensus on 5 domains ("Self-protective behaviors" among others), 6 sub-domains ("Preventing infection" among others), and 15 indicators ("Average hours of daily workplace disinfection by ultraviolet radiation" among others). This study identified a conceptual framework of core behavioral indicators

Layered rare-earth hydroxide and oxide nanoplates of the Y/Tb/Eu system: phase-controlled processing, structure characterization and color-tunable photoluminescence via selective excitation and efficient energy transfer.

PubMed

Wu, Xiaoli; Li, Ji-Guang; Li, Jinkai; Zhu, Qi; Li, Xiaodong; Sun, Xudong; Sakka, Yoshio

2013-02-01

Well-crystallized (Y 0.97- x Tb 0.03 Eu x ) 2 (OH) 5 NO 3 · n H 2 O ( x = 0-0.03) layered rare-earth hydroxide (LRH) nanoflakes of a pure high-hydration phase have been produced by autoclaving from the nitrate/NH 4 OH reaction system under the optimized conditions of 100 °C and pH ∼7.0. The flakes were then converted into (Y 0.97- x Tb 0.03 Eu x ) 2 O 3 phosphor nanoplates with color-tunable photoluminescence. Detailed structural characterizations confirmed that LRH solid solutions contained NO 3 - anions intercalated between the layers. Characteristic Tb 3+ and Eu 3+ emissions were detected in the ternary LRHs by selectively exciting the two types of activators, and the energy transfer from Tb 3+ to Eu 3+ was observed. Annealing the LRHs at 1100 °C produced cubic-lattice (Y 0.97- x Tb 0.03 Eu x ) 2 O 3 solid-solution nanoplates with exposed 222 facets. Multicolor, intensity-adjustable luminescence was attained by varying the excitation wavelength from ∼249 nm (the charge transfer excitation band of Eu 3+ ) to 278 nm (the 4f 8 -4f 7 5d 1 transition of Tb 3+ ). Unitizing the efficient Tb 3+ to Eu 3+ energy transfer, the emission color of (Y 0.97- x Tb 0.03 Eu x ) 2 O 3 was tuned from approximately green to yellowish-orange by varying the Eu 3+ /Tb 3+ ratio. At the optimal Eu 3+ content of x = 0.01, the efficiency of energy transfer was ∼91% and the transfer mechanism was suggested to be electric multipole interactions. The phosphor nanoplates developed in this work may be incorporated in luminescent films and find various lighting and display applications.

Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

PubMed

Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

2016-01-01

One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome Editing of Structural Variations: Modeling and Gene Correction.

PubMed

Park, Chul-Yong; Sung, Jin Jea; Kim, Dong-Wook

2016-07-01

The analysis of chromosomal structural variations (SVs), such as inversions and translocations, was made possible by the completion of the human genome project and the development of genome-wide sequencing technologies. SVs contribute to genetic diversity and evolution, although some SVs can cause diseases such as hemophilia A in humans. Genome engineering technology using programmable nucleases (e.g., ZFNs, TALENs, and CRISPR/Cas9) has been rapidly developed, enabling precise and efficient genome editing for SV research. Here, we review advances in modeling and gene correction of SVs, focusing on inversion, translocation, and nucleotide repeat expansion. Copyright © 2016 Elsevier Ltd. All rights reserved.

In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.

PubMed

Dai, Xinghong; Li, Zhihai; Lai, Mason; Shu, Sara; Du, Yushen; Zhou, Z Hong; Sun, Ren

2017-01-05

Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-coat protein interactions among 15 of these stem-loops with diverse sequences. The stem-loop at the 3' end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.

Knowledge of tuberculosis (TB) and human immunodeficiency virus (HIV) and perception about provider initiated HIV testing and counselling among TB patients attending health facilities in Harar town, Eastern Ethiopia.

PubMed

Seyoum, Ayichew; Legesse, Mengistu

2013-02-08

Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection is one of the major health problems in Ethiopia. The national TB and HIV control guideline in Ethiopia recommends provider initiated HIV testing and counselling (PITC) as a routine care for TB patients. However, the impact of this approach on the treatment seeking of TB patients has not been well studied. In this study, we assessed knowledge of TB and HIV, and perception about PITC among TB patients attending health facilities in Harar town, Eastern Ethiopia. In a health facilities based cross-sectional study, a total of 415 study participants were interviewed about knowledge of TB and HIV as well as the impact of HIV testing on their treatment seeking behavior using a semi-structured questionnaires. Multivariable logistic regression analysis showed the association of distance > 10 km from health facility [adjusted odds ratio (AOR)=0.48, 95% CI: 0.24 - 0.97, P=0.042] with low knowledge of TB. Distance > 10 km from health facility (AOR= 0.12, 95% CI: 0.06 -0.23, P < 0.001) was also associated with low knowledge of HIV testing. Delay in treatment seeking was associated with female participants (AOR = 0.11, 95% CI: 0.05-0.25, <0.001), single marital status (AOR =0.001, 95% CI: 0.00 - 0.01, P< 0.001) and distance > 10 km from health facility (AOR =0.46, 95% CI: 0.28 - 0.75, P=0.002). Most of the study participants (70%) believed that there is no association between TB and HIV/AIDS. On the other hand, two thirds (66.5%) of the participants thought that HIV testing has importance for TB patients. However, the majority (81.6%) of the study participants in the age category less than 21 years believed that fear of PITC could cause delay in treatment seeking. The study showed the association of low knowledge of the study participants about TB and HIV testing with distance > 10 km from health facility. Study participants in the age category less than 21 years thought that fear of PITC could cause treatment

Prevalence of pulmonary TB and spoligotype pattern of Mycobacterium tuberculosis among TB suspects in a rural community in Southwest Ethiopia

PubMed Central

2012-01-01

Background In Ethiopia where there is no strong surveillance system and state of the art diagnostic facilities are limited, the real burden of tuberculosis (TB) is not well known. We conducted a community based survey to estimate the prevalence of pulmonary TB and spoligotype pattern of the Mycobacterium tuberculosis isolates in Southwest Ethiopia. Methods A total of 30040 adults in 10882 households were screened for pulmonary TB in Gilgel Gibe field research centre in Southwest Ethiopia. A total of 482 TB suspects were identified and smear microscopy and culture was done for 428 TB suspects. Counseling and testing for HIV/AIDS was done for all TB suspects. Spoligotyping was done to characterize the Mycobacterium tuberculosis isolates. Results Majority of the TB suspects were females (60.7%) and non-literates (83.6%). Using smear microscopy, a total of 5 new and 4 old cases of pulmonary TB cases were identified making the prevalence of TB 30 per 100,000. However, using the culture method, we identified 17 new cases with a prevalence of 76.1 per 100,000. There were 4.3 undiagnosed pulmonary TB cases for every TB case who was diagnosed through the passive case detection mechanism in the health facility. Eleven isolates (64.7%) belonged to the six previously known spoligotypes: T, Haarlem and Central-Asian (CAS). Six new spoligotype patterns of Mycobacterium tuberculosis, not present in the international database (SpolDB4) were identified. None of the rural residents was HIV infected and only 5 (5.5%) of the urban TB suspects were positive for HIV. Conclusion The prevalence of TB in the rural community of Southwest Ethiopia is low. There are large numbers of undiagnosed TB cases in the community. However, the number of sputum smear-positive cases was very low and therefore the risk of transmitting the infection to others may be limited. Active case finding through health extension workers in the community can improve the low case detection rate in Ethiopia. A large

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

PubMed

Wollenberg, Kurt R; Desjardins, Christopher A; Zalutskaya, Aksana; Slodovnikova, Vervara; Oler, Andrew J; Quiñones, Mariam; Abeel, Thomas; Chapman, Sinead B; Tartakovsky, Michael; Gabrielian, Andrei; Hoffner, Sven; Skrahin, Aliaksandr; Birren, Bruce W; Rosenthal, Alexander; Skrahina, Alena; Earl, Ashlee M

2017-02-01

The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB. Using a phylogenomic approach, we estimated that the majority of MDR-TB was due to the recent transmission of already-resistant M. tuberculosis strains rather than repeated de novo evolution of resistance within patients, while XDR-TB was acquired through both routes. Longitudinal sampling of M. tuberculosis from 34 patients with treatment failure showed that most strains persisted genetically unchanged during treatment or acquired resistance to fluoroquinolones. HIV+ patients were significantly more likely to have multiple infections over time than HIV- patients, highlighting a specific need for careful infection control in these patients. These data provide a better understanding of the genomic composition, transmission, and evolution of MDR- and XDR-TB in Belarus and will enable improved diagnostics, treatment protocols, and prognostic decision-making. Copyright © 2017 Wollenberg et al.

HIV-TB Coinfection among 57 Million Pregnant Women, Obstetric Complications, Alcohol Use, Drug Abuse, and Depression.

PubMed

Fernandez, Dorian; Salami, Imoleayo; Davis, Janelle; Mbah, Florence; Kazeem, Aisha; Ash, Abreah; Babino, Justin; Carter, Laquiesha; Salemi, Jason L; Spooner, Kiara K; Olaleye, Omonike A; Salihu, Hamisu M

2018-01-01

HIV and tuberculosis represent diseases of major public health importance worldwide. Very little is known about HIV-TB coinfection among pregnant women, especially from industrialized settings. In this study, we examined the association between TB, HIV, and HIV-TB coinfection among pregnant mothers and obstetric complications, alcohol use, drug abuse, and depression. We examined inpatient hospital discharges in the United States from January 1, 2002, through December 31, 2014. We employed multivariable survey logistic regression to generate adjusted estimates for the association between infection status and study outcomes. We analyzed approximately 57 million records of pregnant women and their delivery information. HIV-TB coinfection was associated with the highest risks for several obstetric complications, alcohol use, and drug abuse. The risk for alcohol abuse was more than twice as high among HIV-monoinfected as compared to TB-monoinfected mothers. That risk gap more than doubled with HIV-TB coinfection. Both HIV-monoinfected and HIV-TB coinfected mothers experienced similarly increased risks for depression. Mothers with HIV-TB coinfection experienced relatively heightened risks for obstetric complications, alcohol use, and drug abuse. The findings of this study underscore the importance of augmenting and enhancing social and structural support systems for HIV-TB coinfected pregnant women.

Team approach to manage difficult-to-treat TB cases: Experiences in Europe and beyond.

PubMed

D'Ambrosio, L; Bothamley, G; Caminero Luna, J A; Duarte, R; Guglielmetti, L; Muñoz Torrico, M; Payen, M C; Saavedra Herrera, N; Salazar Lezama, M A; Skrahina, A; Tadolini, M; Tiberi, S; Veziris, N; Migliori, G B

As recommended by the World Health Organization (WHO), optimal management of MDR-TB cases can be ensured by a multi-speciality consultation body known as 'TB Consilium'. This body usually includes different medical specialities, competences and perspectives (e.g., clinical expertise both for adults and children; surgical, radiological and public health expertise; psychological background and nursing experience, among others), thus lowering the risk of making mistakes - or managing the patients inappropriately, in order to improve their clinical outcomes. At present, several high MDR-TB burden countries in the different WHO regions (and beyond) have introduced TB Consilium-like bodies at the national or subnational level to reach consensus on the best treatment approach for their patients affected by TB. In addition, in countries/settings where a formal system of consultation does not exist, specialized staff from MDR-TB reference centres or international organizations usually spend a considerable amount of their working time responding to phone or e-mail clinical queries on how to manage M/XDR-TB cases. The aim of this manuscript is to describe the different experiences with the TB Consilia both at the international level (European Respiratory Society - ERS/WHO TB Consilium) and in some of the countries where this experience operates successfully in Europe and beyond. The Consilium experiences are described around the following topics: (1) history, aims and focus; (2) management and funding; (3) technical functioning and structure; (4) results achieved. In addition a comparative analysis of the TB Consilia in the different countries has been performed. Copyright © 2017 Sociedade Portuguesa de Pneumologia. Published by Elsevier España, S.L.U. All rights reserved.

Divergent Small Tim Homologues Are Associated with TbTim17 and Critical for the Biogenesis of TbTim17 Protein Complexes in Trypanosoma brucei

PubMed Central

Smith, Joseph T.; Singha, Ujjal K.; Misra, Smita

2018-01-01

ABSTRACT The small Tim proteins belong to a group of mitochondrial intermembrane space chaperones that aid in the import of mitochondrial inner membrane proteins with internal targeting signals. Trypanosoma brucei, the protozoan parasite that causes African trypanosomiasis, possesses multiple small Tim proteins that include homologues of T. brucei Tim9 (TbTim9) and Tim10 (TbTim10) and a unique small Tim that shares homology with both Tim8 and Tim13 (TbTim8/13). Here, we found that these three small TbTims are expressed as soluble mitochondrial intermembrane space proteins. Coimmunoprecipitation and mass spectrometry analysis showed that the small TbTims stably associated with each other and with TbTim17, the major component of the mitochondrial inner membrane translocase in T. brucei. Yeast two-hybrid analysis indicated direct interactions among the small TbTims; however, their interaction patterns appeared to be different from those of their counterparts in yeast and humans. Knockdown of the small TbTims reduced cell growth and decreased the steady-state level of TbTim17 and T. brucei ADP/ATP carrier (TbAAC), two polytopic mitochondrial inner membrane proteins. Knockdown of small TbTims also reduced the matured complexes of TbTim17 in mitochondria. Depletion of any of the small TbTims reduced TbTim17 import moderately but greatly hampered the stability of the TbTim17 complexes in T. brucei. Altogether, our results revealed that TbTim9, TbTim10, and TbTim8/13 interact with each other, associate with TbTim17, and play a crucial role in the integrity and maintenance of the levels of TbTim17 complexes. IMPORTANCE Trypanosoma brucei is the causative agent of African sleeping sickness. The parasite’s mitochondrion represents a useful source for potential chemotherapeutic targets. Similarly to yeast and humans, mitochondrial functions depend on the import of proteins that are encoded in the nucleus and made in the cytosol. Even though the machinery involved in this

Divergent Small Tim Homologues Are Associated with TbTim17 and Critical for the Biogenesis of TbTim17 Protein Complexes in Trypanosoma brucei.

PubMed

Smith, Joseph T; Singha, Ujjal K; Misra, Smita; Chaudhuri, Minu

2018-06-27

The small Tim proteins belong to a group of mitochondrial intermembrane space chaperones that aid in the import of mitochondrial inner membrane proteins with internal targeting signals. Trypanosoma brucei , the protozoan parasite that causes African trypanosomiasis, possesses multiple small Tim proteins that include homologues of T. brucei Tim9 (TbTim9) and Tim10 (TbTim10) and a unique small Tim that shares homology with both Tim8 and Tim13 (TbTim8/13). Here, we found that these three small TbTims are expressed as soluble mitochondrial intermembrane space proteins. Coimmunoprecipitation and mass spectrometry analysis showed that the small TbTims stably associated with each other and with TbTim17, the major component of the mitochondrial inner membrane translocase in T. brucei Yeast two-hybrid analysis indicated direct interactions among the small TbTims; however, their interaction patterns appeared to be different from those of their counterparts in yeast and humans. Knockdown of the small TbTims reduced cell growth and decreased the steady-state level of TbTim17 and T. brucei ADP/ATP carrier (TbAAC), two polytopic mitochondrial inner membrane proteins. Knockdown of small TbTims also reduced the matured complexes of TbTim17 in mitochondria. Depletion of any of the small TbTims reduced TbTim17 import moderately but greatly hampered the stability of the TbTim17 complexes in T. brucei Altogether, our results revealed that TbTim9, TbTim10, and TbTim8/13 interact with each other, associate with TbTim17, and play a crucial role in the integrity and maintenance of the levels of TbTim17 complexes. IMPORTANCE Trypanosoma brucei is the causative agent of African sleeping sickness. The parasite's mitochondrion represents a useful source for potential chemotherapeutic targets. Similarly to yeast and humans, mitochondrial functions depend on the import of proteins that are encoded in the nucleus and made in the cytosol. Even though the machinery involved in this

TB-IRIS and remodelling of the T cell compartment in highly immunosuppressed HIV+ patients with TB: the CAPRI T (ANRS-12614) study

PubMed Central

Haridas, V.; Pean, P.; Jasenosky, L.D.; Madec, Y.; Laureillard, D.; Sok, T.; Sath, S.; Borand, L.; Marcy, O.; Chan, S.; Tsitsikov, E.; Delfraissy, J.-F.; Blanc, F.-X.; Goldfeld, A.E.

2015-01-01

Objective To investigate the impact of tuberculosis (TB)-associated immune reconstitution syndrome (IRIS) upon immunological recovery and the T cell compartment after initiation of TB and antiretroviral therapy (ART). Design and methods We prospectively evaluated T cell immunophenotypes by flow cytometry and cytokines by Luminex assays in a subset (n=154) of highly immunosuppressed HIV+ patients with TB from the CAMELIA randomized clinical trial. We compared findings from patients who developed TB-IRIS to findings from patients who did not develop TB-IRIS. Data were evaluated with mixed effect linear regression, Kaplan-Meier estimates, and Wilcoxon rank sum tests, and q-values were calculated to control for multiple comparisons. Results Development of TB-IRIS was associated with significantly greater pre-ART frequencies of HLA-DR+CD45RO+CD4+, CCR5+CD4+, OX40+CD4+, and Fas+ effector memory (EM) CD8+ T cells, and significantly elevated levels of plasma IL-6, IL-1β, IL-8, and IL-10 and viral load. Post-ART initiation, EM CD4+ and Fas+ EM CD4+ T cell frequencies significantly expanded, and central memory (CM) CD4+ T cell frequencies significantly contracted in patients who experienced TB-IRIS. By week 34 post-TB treatment initiation, EM/CM CD4+ T cell ratios were markedly higher in TB-IRIS versus non-TB-IRIS patients. Conclusions A distinct pattern of pre-ART T cell and cytokine markers appear to poise the immune response to develop TB-IRIS. Experience of TB-IRIS is then associated with long-term remodeling of the CD4+ T cell memory compartment towards an EM-dominated phenotype. We speculate that these pre- and post-ART TB-IRIS-associated immune parameters may contribute to superior immune control of TB/HIV co-infection and better clinical outcome. PMID:25486415

Litigation as TB Rights Advocacy

PubMed Central

2016-01-01

Abstract One thousand people die every day in India as a result of TB, a preventable and treatable disease, even though the Constitution of India, government schemes, and international law guarantee available, accessible, acceptable, quality health care. Failure to address the spread of TB and to provide quality treatment to all affected populations constitutes a public health and human rights emergency that demands action and accountability. As part of a broader strategy, health activists in India employ Public Interest Litigation (PIL) to hold the state accountable for rights violations and to demand new legislation, standards for patient care, accountability for under-spending, improvements in services at individual facilities, and access to government entitlements in marginalized communities. Taking inspiration from right to health PIL cases (PILs), lawyers in a New Delhi-based rights organization used desk research, fact-findings, and the Right To Information Act to build a TB PIL for the Delhi High Court, Sanjai Sharma v. NCT of Delhi and Others (2015). The case argues that inadequate implementation of government TB schemes violates the Constitutional rights to life, health, food, and equality. Although PILs face substantial challenges, this paper concludes that litigation can be a crucial advocacy and accountability tool for people living with TB and their allies. PMID:27781000

Towards the development of new phosphors with reduced content of rare earth elements: Structural and optical characterization of Ce:Tb: Al{sub 2}SiO{sub 5}

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

Chiriu, D.; Stagi, L.; Carbonaro, C.M.

2016-05-15

Highlights: • A new promising inert matrix as host of luminescent ions is proposed. • Al2SiO5 matrix is free from Rare earths (critical raw materials). • Doping the matrix with Ce and Tb we obtain an efficient green emitter. • Cerium acts as sensitizer for Terbium emission. - Abstract: A new promising inert matrix as host of luminescent ions is proposed. Al2SiO5 samples, doped with rare earths (Ce, Tb single doped and co-doped) are proposed as good prospect for the development of new UV–vis converter with reduced content of rare earths elements. Structural characterization by Raman, XRD spectroscopy and TEMmore » imaging reveals the sillimanite phase and nano sized dimension of the investigated powders. Optical characterization by steady time and time resolved emission spectroscopy for the single doped and co-doped samples allows to identify an efficient energy transfer from Ce to Tb ions under near UV excitation wavelength. The intense green emission observed in the Ce:Tb co-doped Al2SiO5 system suggests its potential application as efficient blue pumped green emitter phosphor to be exploited for white LED: to this purpose we tested the compound in combination with a red emitting doping ion recording for Ce:Tb:Cr:ASO system a correlated color temperature of 6720 K.« less

Phase transition of intermetallic TbPt at high temperature and high pressure

NASA Astrophysics Data System (ADS)

Qin, Fei; Wu, Xiang; Yang, Ke; Qin, Shan

2018-04-01

Here we present synchrotron-based x-ray diffraction experiments combined with diamond anvil cell and laser heating techniques on the intermetallic rare earth compound TbPt (Pnma and Z  =  4) up to 32.5 GPa and ~1800 K. The lattice parameters of TbPt exhibit continuous compression behavior up to 18.2 GPa without any evidence of phase transformation. Pressure-volume data were fitted to a third-order Birch-Murnaghan equation of state with V 0  =  175.5(2) Å3, {{K}{{T0}}}   =  110(5) GPa and K{{T0}}\\prime   =  3.8(7). TbPt exhibits anisotropic compression with β a   >  β b   >  β c and the ratio of axial compressibility is 2.50:1.26:1.00. A new monoclinic phase of TbPt assigned to the Pc or P2/c space group was observed at 32.5 GPa after laser heating at ~1800 K. This new phase is stable at high pressure and presented a quenchable property on decompression to ambient conditions. The pressure-volume relationship is well described by the second-order Birch-Murnaghan equation of state, which yields V 0  =  672(4) Å3, {{K}{{T0}}}   =  123(6) GPa, which is about ~14% more compressible than the orthorhombic TbPt. Our results provide more information on the structure and elastic property view, and thus a better understanding of the physical properties related to magnetic structure in some intermetallic rare earth alloys.

Sensitivity and specificity of QuantiFERON-TB Gold Plus compared with QuantiFERON-TB Gold In-Tube and T-SPOT.TB on active tuberculosis in Japan.

PubMed

Takasaki, Jin; Manabe, Toshie; Morino, Eriko; Muto, Yoshikazu; Hashimoto, Masao; Iikura, Motoyasu; Izumi, Shinyu; Sugiyama, Haruhito; Kudo, Koichiro

2018-03-01

The QuantiFERON-TB Gold Plus (QFT-Plus) was introduced in 2015 as a new generation of interferon-gamma release assays (IGRAs) designed to detect Mycobacterium tuberculosis infection (TB). Examination of its diagnostic accuracy is crucial before it is launched in Japan. We examined 99 patients with laboratory-confirmed active TB (patients) and 117 healthy volunteers with no risk of TB infection (controls) at a medical center in Tokyo, Japan. Blood samples were collected from both the patients and controls and tested using three types of IGRAs: the QFT-Plus, the QuantiFERON-TB Gold In-Tube (QFT-GIT), and the T-SPOT.TB (T-SPOT). The sensitivity and specificity of each IGRA were examined and compared. The sensitivity of the QFT-Plus was 98.9% (95% confidence interval [CI], 0.934-0.998) and similar to that of the QFT-GIT (97.9%; 95% CI, 0.929-0.998) and T-SPOT (96.9%; 95% CI, 0.914-0.994). The specificity of the QFT-Plus was the same as that of the QFT-GIT and T-SPOT (98.1%; 95% CI, 0.934-0.998). One patient with uncontrolled diabetes mellitus showed negative results on all three IGRAs. The QFT-Plus showed a high degree of agreement with the QFT-GIT and T-SPOT, with high sensitivity and specificity. Severe diabetes mellitus may influence the results of IGRAs. Larger studies are needed to validate the accuracy of the GFT-Plus and determine whether it can contribute as adjunctive method for the early diagnosis of active TB in Japan. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Insights on the origin of the Tb5Ge4 magnetocaloric effect

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

Belo, J. H.; Barbosa, M. B.; Pires, A. L.

2017-05-01

In this report the magnetic, atomic structures and spin-lattice coupling have been thoroughly studied through high magnetic field magnetometry, Synchrotron X-ray diffraction under applied magnetic field and magnetostriction measurements in the Tb5Ge4 compounds. A field induced phase transition from an antiferromagnetic towards a ferromagnetic ordering was confirmed but with absence of structural transformation. This absence has been confirmed experimentally through synchrotron x-ray diffraction under applied field (up to 30 T). Moreover, this absence was explained via a thermodynamic free energy model: first principles calculations determined a large energy gap (ΔE=0.65 eV) between the two possible structures, O(I) and O(II). Frommore » magnetic and structural properties, a H-T phase diagram has been proposed for Tb5Ge4. Finally it was observed a large magnetostriction (up to 600 ppm) induced by ΔH=7 T.« less

Pathway to care for drug resistant tuberculosis cases identified during a retrospective study conducted in high TB burden wards in Mumbai.

PubMed

Lobo, Eunice; Shah, Shimoni; Rangan, Sheela; Dholakia, Yatin; Mistry, Nerges

2018-05-10

Background: Mumbai is witnessing a rising incidence of all forms of drug resistant tuberculosis (DR-TB). Methods: A population-based, retrospective study was conducted between April and July 2014, in 15 high TB burden wards in Mumbai, to capture the patient pathways to TB care. A total of 23 DR-TB patients were identified and their pathways to access DR-TB care were recorded using semi-structured interviews. Results: The total DR-TB pathway time of new patients (who did not report any past episode of TB) (180 days; IQR 123,346) was found to be more than twice that of retreatment patients (who reported a past episode of TB) (69 days; IQR 42,128). Conclusions: The unacceptable delay for diagnosis and treatment of DR-TB in Mumbai advocates for consistent implementation of early screening of patients using rapid gene-based technologies.

Clearing the smoke around the TB-HIV syndemic: smoking as a critical issue for TB and HIV treatment and care

PubMed Central

Jackson-Morris, A.; Fujiwara, P. I.; Pevzner, E.

2016-01-01

SUMMARY The collision of the tuberculosis (TB) and human immunodeficiency virus (HIV) epidemics has been described as a ‘syndemic’ due to the synergistic impact on the burden of both diseases. This paper explains the urgent need for practitioners and policy makers to address a third epidemic that exacerbates TB, HIV and TB-HIV. Tobacco use is the leading cause of preventable death worldwide. Smoking is more prevalent among persons diagnosed with TB or HIV. Smoking is associated with tuberculous infection, TB disease and poorer anti-tuberculosis treatment outcomes. It is also associated with an increased risk of smoking-related diseases among people living with HIV, and smoking may also inhibit the effectiveness of life-saving ART. In this paper, we propose integrating into TB and HIV programmes evidence-based strategies from the ‘MPO-WER’ package recommended by the World Health Organization’s Framework Convention on Tobacco Control. Specific actions that can be readily incorporated into current practice are recommended to improve TB and HIV outcomes and care, and reduce the unnecessary burden of death and disease due to smoking. PMID:26260816

Chromosome rearrangements and the evolution of genome structuring and adaptability.

PubMed

Crombach, Anton; Hogeweg, Paulien

2007-05-01

Eukaryotes appear to evolve by micro and macro rearrangements. This is observed not only for long-term evolutionary adaptation, but also in short-term experimental evolution of yeast, Saccharomyces cerevisiae. Moreover, based on these and other experiments it has been postulated that repeat elements, retroposons for example, mediate such events. We study an evolutionary model in which genomes with retroposons and a breaking/repair mechanism are subjected to a changing environment. We show that retroposon-mediated rearrangements can be a beneficial mutational operator for short-term adaptations to a new environment. But simply having the ability of rearranging chromosomes does not imply an advantage over genomes in which only single-gene insertions and deletions occur. Instead, a structuring of the genome is needed: genes that need to be amplified (or deleted) in a new environment have to cluster. We show that genomes hosting retroposons, starting with a random order of genes, will in the long run become organized, which enables (fast) rearrangement-based adaptations to the environment. In other words, our model provides a "proof of principle" that genomes can structure themselves in order to increase the beneficial effect of chromosome rearrangements.

Extensively drug-resistant tuberculosis (XDR-TB) in Morocco.

PubMed

Ennassiri, Wifak; Jaouhari, Sanae; Cherki, Wafa; Charof, Reda; Filali-Maltouf, Abdelkarim; Lahlou, Ouafae

2017-12-01

Extensively drug-resistant tuberculosis (XDR-TB) has recently been identified as a major global health threat. The aim of this study was to evaluate the presence of XDR-TB among Mycobacterium tuberculosis isolates in Morocco and its association with demographic, clinical and epidemiological features. A total of 524 patients from the Moroccan National Tuberculosis Reference Laboratory, representative of all of the geographic regions, were subject to first-line drug susceptibility testing (DST). Subsequently, 155 isolates found to be multidrug-resistant tuberculosis (MDR-TB) underwent second-line DST. Moreover, to enhance our understanding of the genetic basis of these drug-resistant strains, drug resistance-associated mutations were investigated in isolates either identified as pre-XDR- and XDR-TB or suspected resistant using the GenoType ® MTBDRsl V1.0 assay. In this study, 4 (2.6%) XDR-TB and 18 (11.6%) pre-XDR-TB isolates were identified. Agreement between the MTBDRsl assay results and phenotypic DST was 95.2% for ofloxacin, 81.0% for kanamycin and 95.2% for amikacin. To the best of our knowledge, this is the first study to evaluate the frequency of XDR-TB in Morocco. These results highlight the need to reinforce the TB management policy in Morocco with regard to control and detection strategies in order to prevent further spread of XDR-TB isolates. Copyright © 2017. Published by Elsevier Ltd.

TB in Vulnerable Populations

PubMed Central

Ugarte-Gil, César; Caro, Godofredo; Aylas, Rula; Castro, César; Lema, Claudia

2016-01-01

Abstract This article analyzes the factors associated with vulnerability of the Ashaninka, the most populous indigenous Peruvian Amazonian people, to tuberculosis (TB). By applying a human rights-based analytical framework that assesses public policy against human rights standards and principles, and by offering a step-by-step framework for a full assessment of compliance, it provides evidence of the relationship between the incidence of TB among the Ashaninka and Peru’s poor level of compliance with its human rights obligations. The article argues that one of the main reasons for the historical vulnerability of the Ashaninka to diseases such as TB is a lack of political will on the part of the national government to increase public health spending, ensure that resources reach the most vulnerable population, and adopt and invest in a culturally appropriate health system. PMID:27780999

World TB Day 2018: The Challenge of Drug Resistant Tuberculosis.

PubMed

Gupta-Wright, Ankur; Tomlinson, Gillian S; Rangaka, Molebogeng X; Fletcher, Helen A

2018-01-01

On 24th March, the world commemorates the day in 1882 when Dr Robert Koch announced his discovery of Mycobacterium tuberculosis (MTB). Over 130 years later, tuberculosis (TB) continues to affect individuals, communities, and entire health systems and economies. Koch unsuccessfully tried to 'cure' TB, and despite major advances in other areas of medicine, control of TB remains elusive- in 2016 TB was the leading infectious cause of death. The STOP TB partnership and World Health Organization (WHO) have announced their theme for World TB Day 2018 "Wanted: Leaders for a TB-Free World. You can make history. End TB." This theme recognizes that TB is much larger than any one person, institute or discipline of research, and provides an opportunity for us to reflect on the major challenges and consider how we, as a scientific community, can work together and take the lead to address the global crisis of drug-resistant TB (DR-TB).

Progress and challenges in TB vaccine development

PubMed Central

Voss, Gerald; Casimiro, Danilo; Neyrolles, Olivier; Williams, Ann; Kaufmann, Stefan H.E.; McShane, Helen; Hatherill, Mark; Fletcher, Helen A

2018-01-01

The Bacille Calmette Guerin (BCG) vaccine can provide decades of protection against tuberculosis (TB) disease, and although imperfect, BCG is proof that vaccine mediated protection against TB is a possibility. A new TB vaccine is, therefore, an inevitability; the question is how long will it take us to get there? We have made substantial progress in the development of vaccine platforms, in the identification of antigens and of immune correlates of risk of TB disease. We have also standardized animal models to enable head-to-head comparison and selection of candidate TB vaccines for further development.  To extend our understanding of the safety and immunogenicity of TB vaccines we have performed experimental medicine studies to explore route of administration and have begun to develop controlled human infection models. Driven by a desire to reduce the length and cost of human efficacy trials we have applied novel approaches to later stage clinical development, exploring alternative clinical endpoints to prevention of disease outcomes. Here, global leaders in TB vaccine development discuss the progress made and the challenges that remain. What emerges is that, despite scientific progress, few vaccine candidates have entered clinical trials in the last 5 years and few vaccines in clinical trials have progressed to efficacy trials. Crucially, we have undervalued the knowledge gained from our “failed” trials and fostered a culture of risk aversion that has limited new funding for clinical TB vaccine development. The unintended consequence of this abundance of caution is lack of diversity of new TB vaccine candidates and stagnation of the clinical pipeline. We have a variety of new vaccine platform technologies, mycobacterial antigens and animal and human models.  However, we will not encourage progression of vaccine candidates into clinical trials unless we evaluate and embrace risk in pursuit of vaccine development. PMID:29568497

Progress and challenges in TB vaccine development.

PubMed

Voss, Gerald; Casimiro, Danilo; Neyrolles, Olivier; Williams, Ann; Kaufmann, Stefan H E; McShane, Helen; Hatherill, Mark; Fletcher, Helen A

2018-01-01

The Bacille Calmette Guerin (BCG) vaccine can provide decades of protection against tuberculosis (TB) disease, and although imperfect, BCG is proof that vaccine mediated protection against TB is a possibility. A new TB vaccine is, therefore, an inevitability; the question is how long will it take us to get there? We have made substantial progress in the development of vaccine platforms, in the identification of antigens and of immune correlates of risk of TB disease. We have also standardized animal models to enable head-to-head comparison and selection of candidate TB vaccines for further development.  To extend our understanding of the safety and immunogenicity of TB vaccines we have performed experimental medicine studies to explore route of administration and have begun to develop controlled human infection models. Driven by a desire to reduce the length and cost of human efficacy trials we have applied novel approaches to later stage clinical development, exploring alternative clinical endpoints to prevention of disease outcomes. Here, global leaders in TB vaccine development discuss the progress made and the challenges that remain. What emerges is that, despite scientific progress, few vaccine candidates have entered clinical trials in the last 5 years and few vaccines in clinical trials have progressed to efficacy trials. Crucially, we have undervalued the knowledge gained from our "failed" trials and fostered a culture of risk aversion that has limited new funding for clinical TB vaccine development. The unintended consequence of this abundance of caution is lack of diversity of new TB vaccine candidates and stagnation of the clinical pipeline. We have a variety of new vaccine platform technologies, mycobacterial antigens and animal and human models.  However, we will not encourage progression of vaccine candidates into clinical trials unless we evaluate and embrace risk in pursuit of vaccine development.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Technology and tuberculosis control: the OUT-TB Web experience.

PubMed

Guthrie, Jennifer L; Alexander, David C; Marchand-Austin, Alex; Lam, Karen; Whelan, Michael; Lee, Brenda; Furness, Colin; Rea, Elizabeth; Stuart, Rebecca; Lechner, Julia; Varia, Monali; McLean, Jennifer; Jamieson, Frances B

2017-04-01

Develop a tool to disseminate integrated laboratory, clinical, and demographic case data necessary for improved contact tracing and outbreak detection of tuberculosis (TB). In 2007, the Public Health Ontario Laboratories implemented a universal genotyping program to monitor the spread of TB strains within Ontario. Ontario Universal Typing of TB (OUT-TB) Web utilizes geographic information system (GIS) technology with a relational database platform, allowing TB control staff to visualize genotyping matches and microbiological data within the context of relevant epidemiological and demographic data. OUT-TB Web is currently available to the 8 health units responsible for >85% of Ontario's TB cases and is a valuable tool for TB case investigation. Users identified key features to implement for application enhancements, including an e-mail alert function, customizable heat maps for visualizing TB and drug-resistant cases, socioeconomic map layers, a dashboard providing TB surveillance metrics, and a feature for animating the geographic spread of strains over time. OUT-TB Web has proven to be an award-winning application and a useful tool. Developed and enhanced using regular user feedback, future versions will include additional data sources, enhanced map and line-list filter capabilities, and development of a mobile app. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Accelerating access to quality TB care for pediatric TB cases through better diagnostic strategy in four major cities of India.

PubMed

Raizada, Neeraj; Khaparde, Sunil D; Salhotra, Virender Singh; Rao, Raghuram; Kalra, Aakshi; Swaminathan, Soumya; Khanna, Ashwani; Chopra, Kamal Kishore; Hanif, M; Singh, Varinder; Umadevi, K R; Nair, Sreenivas Achuthan; Huddart, Sophie; Prakash, C H Surya; Mall, Shalini; Singh, Pooja; Saha, B K; Denkinger, Claudia M; Boehme, Catharina; Sarin, Sanjay

2018-01-01

Diagnosis of TB in children is challenging, and is largely based on positive history of contact with a TB case, clinical and radiological findings, often without microbiological confirmation. Diagnostic efforts are also undermined by challenges in specimen collection and the limited availability of high sensitivity, rapid diagnostic tests that can be applied with a quick turnaround time. The current project was undertaken in four major cities of India to address TB diagnostic challenges in pediatric population, by offering free of cost Xpert testing to pediatric presumptive TB cases, thereby paving the way for better TB care. A high throughput lab was established in each of the four project cities, and linked to various health care providers across the city through rapid specimen transportation and electronic reporting linkages. Free Xpert testing was offered to all pediatric (0-14 years) presumptive TB cases (both pulmonary and extra-pulmonary) seeking care at public and private health facilities. The current project enrolled 42,238 pediatric presumptive TB cases from April, 2014 to June, 2016. A total of 3,340 (7.91%, CI 7.65-8.17) bacteriologically confirmed TB cases were detected, of which 295 (8.83%, CI 7.9-9.86) were rifampicin-resistant. The level of rifampicin resistance in the project cohort was high. Overall Xpert yielded a high proportion of valid results and TB detection rates were more than three-fold higher than smear microscopy. The project provided same-day testing and early availability of results led to rapid treatment initiation and success rates and very low rates of treatment failure and loss to follow-up. The current project demonstrated the feasibility of rolling out rapid and upfront Xpert testing for pediatric presumptive TB cases through a single Xpert lab per city in an efficient manner. Rapid turnaround testing time facilitated prompt and appropriate treatment initiation. These results suggest that the upfront Xpert assay is a promising

Accelerating access to quality TB care for pediatric TB cases through better diagnostic strategy in four major cities of India

PubMed Central

Raizada, Neeraj; Khaparde, Sunil D.; Salhotra, Virender Singh; Rao, Raghuram; Kalra, Aakshi; Swaminathan, Soumya; Khanna, Ashwani; Chopra, Kamal Kishore; Hanif, M.; Singh, Varinder; Umadevi, K. R.; Nair, Sreenivas Achuthan; Huddart, Sophie; Prakash, C. H. Surya; Mall, Shalini; Singh, Pooja; Saha, B. K.; Denkinger, Claudia M.; Boehme, Catharina

2018-01-01

Background Diagnosis of TB in children is challenging, and is largely based on positive history of contact with a TB case, clinical and radiological findings, often without microbiological confirmation. Diagnostic efforts are also undermined by challenges in specimen collection and the limited availability of high sensitivity, rapid diagnostic tests that can be applied with a quick turnaround time. The current project was undertaken in four major cities of India to address TB diagnostic challenges in pediatric population, by offering free of cost Xpert testing to pediatric presumptive TB cases, thereby paving the way for better TB care. Methods A high throughput lab was established in each of the four project cities, and linked to various health care providers across the city through rapid specimen transportation and electronic reporting linkages. Free Xpert testing was offered to all pediatric (0–14 years) presumptive TB cases (both pulmonary and extra-pulmonary) seeking care at public and private health facilities. Results The current project enrolled 42,238 pediatric presumptive TB cases from April, 2014 to June, 2016. A total of 3,340 (7.91%, CI 7.65–8.17) bacteriologically confirmed TB cases were detected, of which 295 (8.83%, CI 7.9–9.86) were rifampicin-resistant. The level of rifampicin resistance in the project cohort was high. Overall Xpert yielded a high proportion of valid results and TB detection rates were more than three-fold higher than smear microscopy. The project provided same-day testing and early availability of results led to rapid treatment initiation and success rates and very low rates of treatment failure and loss to follow-up. Conclusion The current project demonstrated the feasibility of rolling out rapid and upfront Xpert testing for pediatric presumptive TB cases through a single Xpert lab per city in an efficient manner. Rapid turnaround testing time facilitated prompt and appropriate treatment initiation. These results suggest

Limitations on human rights: are they justifiable to reduce the burden of TB in the era of MDR- and XDR-TB?

PubMed

Boggio, Andrea; Zignol, Matteo; Jaramillo, Ernesto; Nunn, Paul; Pinet, Geneviève; Raviglione, Mario

2008-01-01

Tuberculosis, in all its forms, poses a serious, demonstrable threat to the health of countless individuals as well as to health as a public good. MDR-TB and, in particular, the emergence of XDR-TB, have re-opened the debate on the importance, and nature, of treatment supervision for basic TB control and the management of drug-resistant TB. Enforcing compulsory measures regarding TB patients raises questions of respect for human rights. Yet, international law provides for rights-limiting principles, which would justify enforcing compulsory measures against TB patients who refuse to have diagnostic procedures or who refuse to be monitored and treated once disease is confirmed. This article analyzes under what circumstances compulsory measures for TB patients may be enforced under international law. Compulsory measures for TB patients may, in fact, be justified on legal grounds provided that these measures are foreseen in the law, that they are used as a last resort, and that safeguards are in place to protect affected individuals. The deadly nature of the disease, its epidemiology, the high case fatality rate, and the speed at which the disease leads to death when associated with HIV are proven.

Self-Propagating Combustion Synthesis, Luminescent Properties and Photocatalytic Activities of Pure Ca12Al14O33: Tb3+(Sm3+)

NASA Astrophysics Data System (ADS)

Liu, Rong; Yan, Yongsheng; Ma, Changchang

2018-03-01

The dual-functional Ca12Al14O33: Tb3+ and Ca12Al14O33: Sm3+ materials were prepared by the Self-Propagating Combustion Synthesis (SPCS) technology. The structure, morphology and light absorption property were investigated by XRD、FT-IR、UV-Vis DRS and SEM etc.. The doping of Tb3+ and Sm3+ ions had not changed cubic structure of Ca12Al14O33 but leaded to the slight lattice dilatation and the red-shifts of absorption peaks/edges. The excitation and emission spectra indicated that Ca12Al14O33: Tb3+ and Ca12Al14O33: Sm3+ are superior green and red luminescent materials, respectively, and displayed the distinctly refined structure characteristics which had importantly reference value for the energy level investigation of Tb3+ and Sm3+ ions. Meanwhile, Ca12Al14O33: Tb3+ and Ca12Al14O33: Sm3+ also exhibited the improved photocatalytic degradation for removing dye MB compared with bare Ca12Al14O33.

Pathway to care for drug resistant tuberculosis cases identified during a retrospective study conducted in high TB burden wards in Mumbai

PubMed Central

Lobo, Eunice; Shah, Shimoni; Rangan, Sheela; Dholakia, Yatin; Mistry, Nerges

2018-01-01

Background: Mumbai is witnessing a rising incidence of all forms of drug resistant tuberculosis (DR-TB). Methods: A population-based, retrospective study was conducted between April and July 2014, in 15 high TB burden wards in Mumbai, to capture the patient pathways to TB care. A total of 23 DR-TB patients were identified and their pathways to access DR-TB care were recorded using semi-structured interviews. Results: The total DR-TB pathway time of new patients (who did not report any past episode of TB) (180 days; IQR 123,346) was found to be more than twice that of retreatment patients (who reported a past episode of TB) (69 days; IQR 42,128). Conclusions: The unacceptable delay for diagnosis and treatment of DR-TB in Mumbai advocates for consistent implementation of early screening of patients using rapid gene-based technologies. PMID:29863175

Accelerating TB notification from the private health sector in Delhi, India.

PubMed

Kundu, Debashish; Chopra, Kamal; Khanna, Ashwani; Babbar, Neeti; Padmini, T J

2016-01-01

In India, almost half of all patients with tuberculosis (TB) seek care in the private sector as the first point of care. The national programme is unable to support such TB patients and facilitate effective treatment, as there is no information on TB and Multi or Extensively Drug Resistant TB (M/XDR-TB) diagnosis and treatment in private sector. To improve this situation, Government of India declared TB a notifiable disease for establishing TB surveillance system, to extend supportive mechanism for TB treatment adherence and standardised practices in the private sector. But TB notification from the private sector is a challenge and still a lot needs to be done to accelerate TB notification. Delhi State TB Control Programme had taken initiatives for improving notification of TB cases from the private sector in 2014. Key steps taken were to constitute a state level TB notification committee to oversee the progress of TB notification efforts in the state and direct 'one to one' sensitisation of private practitioners (PPs) (in single PP's clinic, corporate hospitals and laboratories) by the state notification teams with the help of available tools for sensitising the PP on TB notification - TB Notification Government Order, Guidance Tool for TB Notification and Standards of TB Care in India. As a result of focussed state level interventions, without much external support, there was an accelerated notification of TB cases from the private sector. TB notification cases from the private sector rose from 341 (in 2013) to 4049 (by the end of March 2015). Active state level initiatives have led to increase in TB case notification. Copyright © 2016 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

A sequence-based survey of the complex structural organization of tumor genomes

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

Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav

2008-04-03

The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison ofmore » the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.« less

Structured Matrix Completion with Applications to Genomic Data Integration.

PubMed

Cai, Tianxi; Cai, T Tony; Zhang, Anru

2016-01-01

Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed. We provide theoretical justification for the proposed SMC method and derive lower bound for the estimation errors, which together establish the optimal rate of recovery over certain classes of approximately low-rank matrices. Simulation studies show that the method performs well in finite sample under a variety of configurations. The method is applied to integrate several ovarian cancer genomic studies with different extent of genomic measurements, which enables us to construct more accurate prediction rules for ovarian cancer survival.

Current challenges in genome annotation through structural biology and bioinformatics.

PubMed

Furnham, Nicholas; de Beer, Tjaart A P; Thornton, Janet M

2012-10-01

With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry. Copyright © 2012. Published by Elsevier Ltd.

Hydrothermal synthesis of 4ZnO·B2O3·H2O:Ln3 + (Ln = Eu, Tb) phosphors: Morphology-tunable and luminescence properties

NASA Astrophysics Data System (ADS)

Cao, Shiwei; Jiao, Yang; Han, Weifang; Ge, Chunhua; Song, Bo; Wang, Jie; Zhang, Xiangdong

2018-02-01

4ZnO·B2O3·H2O:Ln3 + (Ln = Eu, Tb) phosphors with different morphologies have been successfully synthesized via one-step hydrothermal method through regulating the molar amount of Eu3 + and Tb3 +. Comprehensive scanning electron microscopy (SEM), X-ray diffraction (XRD) Fourier transform infrared spectrum (FT-IR) and inductively coupled plasma atomic emission spectrometer (ICP-AES) characterizations all confirm that obtained products are 4ZnO·B2O3·H2O:Ln3 + (Ln = Eu, Tb). The experimental results displayed that the morphology and photoluminescence of compounds is regularly changed with increased the molar amount of rare earth ions. For the Eu3 +-doped, Tb3 +-doped and Eu3 +/Tb3 + co-doped 4ZnO·B2O3·H2O phosphors of morphologies, the rod-like structures gradually changed to flower-like structures, fine wire-like structure and hybrid structure, respectively. To their photoluminescence, the Eu3 + shows a red emission (615 nm); the Tb3 + shows a green emission (545 nm); for the Eu3 +/Tb3 + co-doped 4ZnO·B2O3·H2O phosphors, a combination of blue (5d-4f of Eu2 +), green (5D4-7F5 of Tb3 +) and red (5D0-7F2 of Eu3 +) emissions emerges to achieve white emission. In addition, the energy transfer among Eu3 +, Eu2 + and Tb3 + ions was also discussed.

Hydrothermal synthesis of 4ZnO·B2O3·H2O:Ln3+ (Ln=Eu, Tb) phosphors: Morphology-tunable and luminescence properties.

PubMed

Cao, Shiwei; Jiao, Yang; Han, Weifang; Ge, Chunhua; Song, Bo; Wang, Jie; Zhang, Xiangdong

2018-02-05

4ZnO·B 2 O 3 ·H 2 O:Ln 3+ (Ln=Eu, Tb) phosphors with different morphologies have been successfully synthesized via one-step hydrothermal method through regulating the molar amount of Eu 3+ and Tb 3+ . Comprehensive scanning electron microscopy (SEM), X-ray diffraction (XRD) Fourier transform infrared spectrum (FT-IR) and inductively coupled plasma atomic emission spectrometer (ICP-AES) characterizations all confirm that obtained products are 4ZnO·B 2 O 3 ·H 2 O:Ln 3+ (Ln=Eu, Tb). The experimental results displayed that the morphology and photoluminescence of compounds is regularly changed with increased the molar amount of rare earth ions. For the Eu 3+ -doped, Tb 3+ -doped and Eu 3+ /Tb 3+ co-doped 4ZnO·B 2 O 3 ·H 2 O phosphors of morphologies, the rod-like structures gradually changed to flower-like structures, fine wire-like structure and hybrid structure, respectively. To their photoluminescence, the Eu 3+ shows a red emission (615nm); the Tb 3+ shows a green emission (545nm); for the Eu 3+ /Tb 3+ co-doped 4ZnO·B 2 O 3 ·H 2 O phosphors, a combination of blue (5d-4f of Eu 2+ ), green ( 5 D 4 - 7 F 5 of Tb 3+ ) and red ( 5 D 0 - 7 F 2 of Eu 3+ ) emissions emerges to achieve white emission. In addition, the energy transfer among Eu 3+ , Eu 2+ and Tb 3+ ions was also discussed. Copyright © 2017. Published by Elsevier B.V.

Monomer and metallopolymer compounds of Tb(III) as precursors for OLEDs

NASA Astrophysics Data System (ADS)

Irina, Savchenko; Oleksandra, Berezhnytska; Olena, Trunova; Yaroslav, Fedorov; Sergiy, Smola; Nataliya, Rusakova

2018-03-01

The Terbium (III) complexes [Tb(III)-water, mixed-ligand complex Tb(III)-phenanthroline] with 2-methyl-5-phenyl-1-pentene-3,5-dione were synthesized. The polycomplex was obtained by free-radical polymerization. The results of above studies have shown that the configuration of the chelate unit is unchanged during the polymerization. As a result, the type of coordination was determined and the structure of coordination polyhedra was assumed. The luminescence spectra of obtained metallocomplexes and polymer were investigated and analyzed. The solubilization of terbium complex with phenanthroline, was shown to change luminescence intensity in this complex.

New drugs and regimens for treatment of TB

PubMed Central

Leibert, Eric; Rom, William N

2013-01-01

Tools for effective TB control have been available for years. Case finding, active medications, case management and directly observed therapy are the foundations for the management of TB. The current TB epidemic, centered in resource-limited settings is fueled by the HIV-1 epidemic. Lack of ability to diagnose and treat drug-resistant TB has led to development of more extensive patterns of resistance. Among the currently available drugs, there is reason to hope that rifamycins paired with fluoroquinolones will lead to shorter treatment regimens for drug-susceptible TB. As the result of novel public-private collaborations and investments of resources, new drugs are being developed. These include TMC207, already shown to have activity early in the treatment of multidrug-resistant TB and others that are likely to be active against persistor organisms, and have the prospect to dramatically shorten treatment courses for active and latent TB. Given that these drugs have novel mechanisms of action, combinations have the prospect to be highly active even against multidrug-resistant organisms. PMID:20586565

Alternative medicine: an ethnographic study of how practitioners of Indian medical systems manage TB in Mumbai.

PubMed

McDowell, Andrew; Pai, Madhukar

2016-03-01

Mumbai is a hot spot for drug-resistant TB, and private practitioners trained in AYUSH systems (Ayurveda, yoga, Unani, Siddha and homeopathy) are major healthcare providers. It is important to understand how AYUSH practitioners manage patients with TB or presumptive TB. We conducted semi-structured interviews of 175 Mumbai slum-based practitioners holding degrees in Ayurveda, homeopathy and Unani. Most providers gave multiple interviews. We observed 10 providers in clinical interactions, documenting: clinical examinations, symptoms, history taking, prescriptions and diagnostic tests. No practitioners exclusively used his or her system of training. The practice of biomedicine is frequent, with practitioners often using biomedical disease categories and diagnostics. The use of homeopathy was rare (only 4% of consultations with homeopaths resulted in homeopathic remedies) and Ayurveda rarer (3% of consultations). For TB, all mentioned chest x-ray while 31 (17.7%) mentioned sputum smear as a TB test. One hundred and sixty-four practitioners (93.7%) reported referring TB patients to a public hospital or chest physician. Eleven practitioners (6.3%) reported treating patients with TB. Nine (5.1%) reported treating patients with drug-susceptible TB with at least one second-line drug. Important sources of health care in Mumbai's slums, AYUSH physicians frequently use biomedical therapies and most refer patients with TB to chest physicians or the public sector. They are integral to TB care and control. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

TB Summit 2014

PubMed Central

Maitra, Arundhati; Bhakta, Sanjib

2014-01-01

World TB Day commemorates Dr Robert Koch’s first announcement on March 24, 1882, that the bacterium Mycobacterium tuberculosis is the causative agent of tuberculosis. Currently, the event comprises of several conferences, meetings and activities held all over the world with the singular intention of raising public awareness about the global health emergency. In spite of having discovered the etiological agent of tuberculosis more than a century ago, a sizeable population still contract the disease every year and fall prey to it. In 2012, an estimated 8.6 million people developed the disease with 1.3 million succumbing to it. The number of TB deaths in children is unacceptably large, given that most are preventable. However, the challenge appears to be shifting toward attempts to control the rise and spread of the drug resistant variants of the microbe. To achieve this, a concerted effort from academia, clinical practice, and industry has been put forth. The TB Summit 2014 attempted to raise awareness as well as bring together experts involved in different aspects of tuberculosis research to help establish a more collective approach to battle this age-old disease. PMID:25003368

Scale-up of collaborative TB/HIV activities in Guyana.

PubMed

Baker, Brian J; Peterson, Brandy; Mohanlall, Jeetendra; Singh, Shanti; Hicks, Collene; Jacobs, Ruth; Ramos, Ruth; Allen, Barbara; Pevzner, Eric

2017-04-20

To assess scale-up of recommended tuberculosis (TB)/HIV activities in Guyana and to identify specific strategies for further expansion. Medical records and clinic registers were reviewed at nine TB clinics and 10 HIV clinics. At TB clinics, data were collected on HIV testing and antiretroviral therapy (ART) for patients with TB/HIV; at HIV clinics, data were collected on intensified case finding (ICF), tuberculin skin test (TST) results, and provision of isoniazid preventive therapy (IPT). At TB clinics, among 461 patients newly diagnosed with TB, 419 (90.9%) had a known HIV status and 121 (28.9%) were HIV-infected. Among the 63 patients with TB/HIV, 33 (52.4%) received ART. Among the 45 patients with TB/HIV for whom dates of HIV diagnosis were available, 38 (84.4%) individuals knew their HIV status prior to TB diagnosis. At HIV clinics, among 127 patients eligible to receive a TST, 87 (68.5%) received a TST, 66 (75.9%) had a TST result, seven (10.6%) had a newly positive result, two had a previously positive result, and six of nine patients with positive results (66.7%) received IPT. ICF could not be assessed because of incomplete or discrepant documentation. An in-depth evaluation of TB/HIV activities successfully identified areas of success and remaining challenges. At TB clinics, HIV testing rates are high; further scale-up of ART for persons with TB/HIV is needed. At HIV clinics, use of TST to focus IPT is a feasible and efficient strategy; improving rates of annual TST screening will allow for further expansion of IPT.

Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

PubMed

Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

2013-01-01

In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Structural genomics reveals EVE as a new ASCH/PUA-related domain

PubMed Central

Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

2014-01-01

Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354

Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

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

Bertonati, C.; Punta, M; Fischer, M

2008-01-01

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE.more » Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.« less

Spectroscopy and energy transfer in lead borate glasses doubly doped with Dy(3)(+)-Tb(3+) and Tb(3)(+)-Eu(3+) ions.

PubMed

Pisarska, Joanna; Kos, Agnieszka; Pisarski, Wojciech A

2014-08-14

Lead borate glasses doubly doped with Dy(3)(+)-Tb(3+) and Tb(3+)-Eu(3+) were investigated using optical spectroscopy. Luminescence spectra of rare earths were detected under various excitation wavelengths. The main green emission band due to (5)D4→(7)F5 transition of Tb(3+) is observed under excitation of Dy(3+), whereas the main red emission band related to (5)D0→(7)F2 transition of Eu(3+) is successfully observed under direct excitation of Tb(3+). In both cases, the energy transfer processes from Dy(3+) to Tb(3+) and from Tb(3+) to Eu(3+) in lead borate glasses occur through a nonradiative processes with efficiencies up to 16% and 18%, respectively. The presence of energy transfer process was also confirmed by excitation spectra measurements. Copyright © 2014 Elsevier B.V. All rights reserved.

Yellow to orange-reddish glass phosphors: Sm3+, Tb3+ and Sm3+/Tb3+ in zinc tellurite-germanate glasses

NASA Astrophysics Data System (ADS)

Alvarez-Ramos, M. E.; Alvarado-Rivera, J.; Zayas, Ma. E.; Caldiño, U.; Hernández-Paredes, J.

2018-01-01

An optical spectroscopy analysis of TeO-GeO2-ZnO glass co-activating Sm3+/Tb3+ ions was carried out through Raman, photoluminescence spectra and decay time profiles as a function of Sm3+ concentration. According to the estimated CIE1931 chromaticity coordinates, the color of the emission can be adjusted from the yellow light region (0.4883, 0.4774), towards the reddish light region (0.5194,0.4144) by increasing the Sm3+ content from 1, 3, 5% mol, co-doped with 1% mol Tb3+ under co-excitation of Sm3+ and Tb3+ at 378 nm. The color temperatures are in the range of 1379-2804 K. Such photoluminescence is generated by the 4G 5/2 → 4H 5/2, 4H 7/2, 4H9/2 emissions of Sm3+ in addition to the 5D4→7F6,5,4,3 emissions of Tb3+; the single doped Sm3+ glass displayed an intense orange light. Meanwhile, co-doped Sm3+/Tb3+ glasses excited at 378 nm showed a significant reduction in Tb3+ emission, with a simultaneous increment in the reddish-orange emission of Sm3+, due to a non-radiative resonant energy transfer from Tb3+ to Sm3+. Decay time profile analysis of the Tb3+ emission as function of Sm3+ ion content suggests that an electric dipole-dipole interaction into Tb3+-Sm3+ clusters might dominate in the energy transfer process, with an efficiency and probability of 0.22, 0.27, 0.38 and 122.8, 327.6, 522.7 s-1, respectively.

Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release.

PubMed

Organtini, Lindsey J; Shingler, Kristin L; Ashley, Robert E; Capaldi, Elizabeth A; Durrani, Kulsoom; Dryden, Kelly A; Makhov, Alexander M; Conway, James F; Pizzorno, Marie C; Hafenstein, Susan

2017-01-15

The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-like conformation for the procapsid and genome-filled capsids, whereas the putative A-particle and empty capsids that had released the genome had a closed tube-like spike conformation. Between the two conformations, the spikes undergo a significant hinge-like movement that we predicted using a Robetta model of the structure comprising the spike. We conclude that the spike structures likely serve a function during host entry, changing conformation to release the genome, and that the genome may escape from a 5-fold vertex to initiate infection. Finally, the structures illustrate that, similarly to picornaviruses, DWV forms alternate particle conformations implicated in assembly, host attachment, and RNA release. Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ectoparasitic mite Varroa destructor have been linked to colony collapse disorder. DWV was purified from infected adult worker bees to pursue biochemical and structural studies that allowed the first glimpse into the conformational changes that may be required during transmission and genome release for DWV. Copyright © 2017 American Society for Microbiology.

Use of Xpert MTB/RIF in Decentralized Public Health Settings and Its Effect on Pulmonary TB and DR-TB Case Finding in India.

PubMed

Sachdeva, Kuldeep Singh; Raizada, Neeraj; Sreenivas, Achuthan; Van't Hoog, Anna H; van den Hof, Susan; Dewan, Puneet K; Thakur, Rahul; Gupta, R S; Kulsange, Shubhangi; Vadera, Bhavin; Babre, Ameet; Gray, Christen; Parmar, Malik; Ghedia, Mayank; Ramachandran, Ranjani; Alavadi, Umesh; Arinaminpathy, Nimalan; Denkinger, Claudia; Boehme, Catharina; Paramasivan, C N

2015-01-01

Xpert MTB/RIF, the first automated molecular test for tuberculosis, is transforming the diagnostic landscape in high-burden settings. This study assessed the impact of up-front Xpert MTB/RIF testing on detection of pulmonary tuberculosis (PTB) and rifampicin-resistant PTB (DR-TB) cases in India. This demonstration study was implemented in 18 sub-district level TB programme units (TUs) in India in diverse geographic and demographic settings covering a population of 8.8 million. A baseline phase in 14 TUs captured programmatic baseline data, and an intervention phase in 18 TUs had Xpert MTB/RIF offered to all presumptive TB patients. We estimated changes in detection of TB and DR-TB, the former using binomial regression models to adjust for clustering and covariates. In the 14 study TUs, which participated in both phases, 10,675 and 70,556 presumptive TB patients were enrolled in the baseline and intervention phase, respectively, and 1,532 (14.4%) and 14,299 (20.3%) bacteriologically confirmed PTB cases were detected. The implementation of Xpert MTB/RIF was associated with increases in both notification rates of bacteriologically confirmed TB cases (adjusted incidence rate ratio [aIRR] 1.39; CI 1.18-1.64), and proportion of bacteriological confirmed TB cases among presumptive TB cases (adjusted risk ratio (aRR) 1.33; CI 1.6-1.52). Compared with the baseline strategy of selective drug-susceptibility testing only for PTB cases at high risk of drug-resistant TB, Xpert MTB/RIF implementation increased rifampicin resistant TB case detection by over fivefold. Among, 2765 rifampicin resistance cases detected, 1055 were retested with conventional drug susceptibility testing (DST). Positive predictive value (PPV) of rifampicin resistance detected by Xpert MTB/RIF was 94.7% (CI 91.3-98.1), in comparison to conventional DST. Introduction of Xpert MTB/RIF as initial diagnostic test for TB in public health facilities significantly increased case-notification rates of all

Use of Xpert MTB/RIF in Decentralized Public Health Settings and Its Effect on Pulmonary TB and DR-TB Case Finding in India

PubMed Central

Sachdeva, Kuldeep Singh; Raizada, Neeraj; Sreenivas, Achuthan; van't Hoog, Anna H.; van den Hof, Susan; Dewan, Puneet K.; Thakur, Rahul; Gupta, R. S.; Kulsange, Shubhangi; Vadera, Bhavin; Babre, Ameet; Gray, Christen; Parmar, Malik; Ghedia, Mayank; Ramachandran, Ranjani; Alavadi, Umesh; Arinaminpathy, Nimalan; Denkinger, Claudia; Boehme, Catharina; Paramasivan, C. N.

2015-01-01

Background Xpert MTB/RIF, the first automated molecular test for tuberculosis, is transforming the diagnostic landscape in high-burden settings. This study assessed the impact of up-front Xpert MTB/RIF testing on detection of pulmonary tuberculosis (PTB) and rifampicin-resistant PTB (DR-TB) cases in India. Methods This demonstration study was implemented in 18 sub-district level TB programme units (TUs) in India in diverse geographic and demographic settings covering a population of 8.8 million. A baseline phase in 14 TUs captured programmatic baseline data, and an intervention phase in 18 TUs had Xpert MTB/RIF offered to all presumptive TB patients. We estimated changes in detection of TB and DR-TB, the former using binomial regression models to adjust for clustering and covariates. Results In the 14 study TUs, which participated in both phases, 10,675 and 70,556 presumptive TB patients were enrolled in the baseline and intervention phase, respectively, and 1,532 (14.4%) and 14,299 (20.3%) bacteriologically confirmed PTB cases were detected. The implementation of Xpert MTB/RIF was associated with increases in both notification rates of bacteriologically confirmed TB cases (adjusted incidence rate ratio [aIRR] 1.39; CI 1.18-1.64), and proportion of bacteriological confirmed TB cases among presumptive TB cases (adjusted risk ratio (aRR) 1.33; CI 1.6-1.52). Compared with the baseline strategy of selective drug-susceptibility testing only for PTB cases at high risk of drug-resistant TB, Xpert MTB/RIF implementation increased rifampicin resistant TB case detection by over fivefold. Among, 2765 rifampicin resistance cases detected, 1055 were retested with conventional drug susceptibility testing (DST). Positive predictive value (PPV) of rifampicin resistance detected by Xpert MTB/RIF was 94.7% (CI 91.3-98.1), in comparison to conventional DST. Conclusion Introduction of Xpert MTB/RIF as initial diagnostic test for TB in public health facilities significantly increased

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

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

Lang, Daniel; Ullrich, Kristian K.; Murat, Florent

Here, the draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome–scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene– and TE–rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono–centric with peaks of a class of Copia elements potentially coinciding with centromeres. Genemore » body methylation is evident in 5.7% of the protein–coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure–based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant–specific cell growth and tissue organization. The P. patens genome lacks the TE–rich pericentromeric and gene–rich distal regions typical for most flowering plant genomes. More non–seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.« less

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

DOE PAGES

Lang, Daniel; Ullrich, Kristian K.; Murat, Florent; ...

2017-12-13

Here, the draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome–scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene– and TE–rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono–centric with peaks of a class of Copia elements potentially coinciding with centromeres. Genemore » body methylation is evident in 5.7% of the protein–coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure–based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant–specific cell growth and tissue organization. The P. patens genome lacks the TE–rich pericentromeric and gene–rich distal regions typical for most flowering plant genomes. More non–seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.« less

Assessing spatial heterogeneity of MDR-TB in a high burden country

PubMed Central

Jenkins, Helen E.; Plesca, Valeriu; Ciobanu, Anisoara; Crudu, Valeriu; Galusca, Irina; Soltan, Viorel; Serbulenco, Aliona; Zignol, Matteo; Dadu, Andrei; Dara, Masoud; Cohen, Ted

2013-01-01

Multidrug-resistant tuberculosis (MDR-TB) is a major concern in countries of the former Soviet Union. The reported risk of resistance among TB cases in the Republic of Moldova is among the highest in the world. We aimed to produce high-resolution spatial maps of MDR-TB risk and burden in this setting. We analyzed national TB surveillance data collected between 2007 and 2010 in Moldova. High drug susceptibility testing coverage and detailed location data permitted identification of sub-regional areas of higher MDR-TB risk. We investigated whether the distribution of cases with MDR-TB risk factors could explain this observed spatial variation in MDR-TB. 3,447 MDR-TB cases were notified during this period; 24% of new and 62% of previously treated patients had MDR-TB. Nationally, the estimated annual MDR-TB incidence was 54 cases/100,000 persons and >1,000 cases/100,000 persons within penitentiaries. We identified substantial geographic variation in MDR-TB burden and hotspots of MDR-TB. Locations with a higher percentage of previously incarcerated TB cases were at greater risk of being MDR-TB hotspots. Spatial analyses revealed striking geographic heterogeneity of MDR-TB. Methods to identify locations of high MDR-TB risk and burden should allow for better resource allocation and more appropriate targeting of studies to understand local mechanisms driving resistance. PMID:23100496

Luminescence and energy transfer in Lu3Al5O12 scintillators co-doped with Ce3+ and Tb3+.

PubMed

Ogiegło, Joanna M; Zych, Aleksander; Ivanovskikh, Konstantin V; Jüstel, Thomas; Ronda, Cees R; Meijerink, Andries

2012-08-23

Lu(3)Al(5)O(12) (LuAG) doped with Ce(3+) is a promising scintillator material with a high density and a fast response time. The light output under X-ray or γ-ray excitation is, however, well below the theoretical limit. In this paper the influence of codoping with Tb(3+) is investigated with the aim to increase the light output. High resolution spectra of singly doped LuAG (with Ce(3+) or Tb(3+)) are reported and provide insight into the energy level structure of the two ions in LuAG. For Ce(3+) zero-phonon lines and vibronic structure are observed for the two lowest energy 5d bands and the Stokes' shift (2 350 cm(-1)) and Huang-Rhys coupling parameter (S = 9) have been determined. Tb(3+) 4f-5d transitions to the high spin (HS) and low spin (LS) states are observed (including a zero-phonon line and vibrational structure for the high spin state). The HS-LS splitting of 5400 cm(-1) is smaller than usually observed and is explained by a reduction of the 5d-4f exchange coupling parameter J by covalency. Upon replacing the smaller Lu(3+) ion with the larger Tb(3+) ion, the crystal field splitting for the lowest 5d states increases, causing the lowest 5d state to shift below the (5)D(4) state of Tb(3+) and allowing for efficient energy transfer from Tb(3+) to Ce(3+) down to the lowest temperatures. Luminescence decay measurements confirm efficient energy transfer from Tb(3+) to Ce(3+) and provide a qualitative understanding of the energy transfer process. Co-doping with Tb(3+) does not result in the desired increase in light output, and an explanation based on electron trapping in defects is discussed.

Neutron spectroscopic study of crystal field excitations in Tb 2Ti 2O 7 and Tb 2Sn 2O 7

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

Zhang, J.; Fritsch, Katharina; Hao, Z.

2014-04-01

We present time-of-flight inelastic neutron scattering measurements at low temperature on powder samples of the magnetic pyrochlore oxides Tb 2Ti 2O 7 and Tb 2Sn 2O 7. These two materials possess related, but different ground states, with Tb 2Sn 2O 7 displaying "soft" spin ice order below T N approx 0.87 K, while Tb 2Ti 2O 7 enters a hybrid, glassy-spin ice state below T g approx 0.2 K. Our neutron measurements, performed at T = 1.5 K and 30 K, probe the crystal field states associated with the J = 6 states of Tb 3+ within the appropriate Fd3-barmmore » pyrochlore environment. These crystal field states determine the size and anisotropy of the Tb 3+ magnetic moment in each material's ground state, information that is an essential starting point for any description of the low temperature phase behavior and spin dynamics in Tb 2Ti 2O 7 and Tb 2Sn 2O 7. While these two materials have much in common, the cubic stanate lattice is expanded compared to the cubic titanate lattice. As our measurements show, this translates into a factor of approx 2 increase in the crystal field bandwidth of the 2J +1 = 13 states in Tb 2Ti 2O 7 compared with Tb 2Sn 2O 7. Our results are consistent with previous measurements on crystal field states in Tb 2Sn 2O 7, wherein the ground state doublet corresponds primarily to mJ = {vert_bar}+-5> and the first excited state doublet to mJ = {vert_bar}+-4>. In contrast, our results on Tb 2Ti 2O 7 differ markedly from earlier studies, showing that the ground state doublet corresponds to a significant mixture of mJ = {vert_bar}+-5>, mJ = {vert_bar}+-4> and mJ = {vert_bar}+-2>, while the first excited state doublet corresponds to a mixture of mJ = {vert_bar}+-4>, mJ = {vert_bar}+-5> and mJ = {vert_bar}+-1>. We discuss these results in the context of proposed mechanisms for the failure of Tb 2Ti 2O 7 to develop conventional long range order down to 50 mK.« less

The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak.

PubMed

Lalor, Maeve K; Casali, Nicola; Walker, Timothy M; Anderson, Laura F; Davidson, Jennifer A; Ratna, Natasha; Mullarkey, Cathy; Gent, Mike; Foster, Kirsty; Brown, Tim; Magee, John; Barrett, Anne; Crook, Derrick W; Drobniewski, Francis; Thomas, H Lucy; Abubakar, Ibrahim

2018-06-01

We used whole-genome sequencing (WGS) to delineate transmission networks and investigate the benefits of WGS during cluster investigation.We included clustered cases of multidrug-resistant (MDR) tuberculosis (TB)/extensively drug-resistant (XDR) TB linked by mycobacterial interspersed repetitive unit variable tandem repeat (MIRU-VNTR) strain typing or epidemiological information in the national cluster B1006, notified between 2007 and 2013 in the UK. We excluded from further investigation cases whose isolates differed by greater than 12 single nucleotide polymorphisms (SNPs). Data relating to patients' social networks were collected.27 cases were investigated and 22 had WGS, eight of which (36%) were excluded as their isolates differed by more than 12 SNPs to other cases. 18 cases were ruled into the transmission network based on genomic and epidemiological information. Evidence of transmission was inconclusive in seven out of 18 cases (39%) in the transmission network following WGS and epidemiological investigation.This investigation of a drug-resistant TB cluster illustrates the opportunities and limitations of WGS in understanding transmission in a setting with a high proportion of migrant cases. The use of WGS should be combined with classical epidemiological methods. However, not every cluster will be solvable, regardless of the quality of genomic data. Copyright ©ERS 2018.

Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory.

PubMed

Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara; Gardy, Jennifer L

2018-01-01

Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. We used Design Study Methodology-a human centered approach drawn from the information visualization domain-to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders' needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

Adverse Events among HIV/MDR-TB Co-Infected Patients Receiving Antiretroviral and Second Line Anti-TB Treatment in Mumbai, India

PubMed Central

Isaakidis, Petros; Varghese, Bhanumati; Mansoor, Homa; Cox, Helen S.; Ladomirska, Joanna; Saranchuk, Peter; Da Silva, Esdras; Khan, Samsuddin; Paryani, Roma; Udwadia, Zarir; Migliori, Giovanni Battista; Sotgiu, Giovanni; Reid, Tony

2012-01-01

Background Significant adverse events (AE) have been reported in patients receiving medications for multidrug- and extensively-drug-resistant tuberculosis (MDR-TB & XDR-TB). However, there is little prospective data on AE in MDR- or XDR-TB/HIV co-infected patients on antituberculosis and antiretroviral therapy (ART) in programmatic settings. Methods Médecins Sans Frontières (MSF) is supporting a community-based treatment program for drug-resistant tuberculosis in HIV-infected patients in a slum setting in Mumbai, India since 2007. Patients are being treated for both diseases and the management of AE is done on an outpatient basis whenever possible. Prospective data were analysed to determine the occurrence and nature of AE. Results Between May 2007 and September 2011, 67 HIV/MDR-TB co-infected patients were being treated with anti-TB treatment and ART; 43.3% were female, median age was 35.5 years (Interquartile Range: 30.5–42) and the median duration of anti-TB treatment was 10 months (range 0.5–30). Overall, AE were common in this cohort: 71%, 63% and 40% of patients experienced one or more mild, moderate or severe AE, respectively. However, they were rarely life-threatening or debilitating. AE occurring most frequently included gastrointestinal symptoms (45% of patients), peripheral neuropathy (38%), hypothyroidism (32%), psychiatric symptoms (29%) and hypokalaemia (23%). Eleven patients were hospitalized for AE and one or more suspect drugs had to be permanently discontinued in 27 (40%). No AE led to indefinite suspension of an entire MDR-TB or ART regimen. Conclusions AE occurred frequently in this Mumbai HIV/MDR-TB cohort but not more frequently than in non-HIV patients on similar anti-TB treatment. Most AE can be successfully managed on an outpatient basis through a community-based treatment program, even in a resource-limited setting. Concerns about severe AE in the management of co-infected patients are justified, however, they should not cause delays

More significance of TB-IGRA except for the diagnose of tuberculosis.

PubMed

Xu, Jun-Chi; Li, Ze-Yi; Chen, Xin-Nian; Shi, Cui-Lin; Wu, Mei-Ying; Chen, Hui; Zhu, Xiao-Yan; Song, Hua-Feng; Wu, Min-Juan; Xu, Ping

2018-01-01

Tuberculosis (TB)-interferon gamma release assay (IGRA) test has the characteristics of short time, high specificity, and high sensitivity, but it lacks the correlation research between TB-IGRA test results and body's immune cells, disease progression and prognosis, which is explored in this study. A retrospective study was carried out on positive TB-IGRA patients who were infected with TB and diagnosed at our hospital from January 2014 to June 2015. The TB-IGRA, routine blood test, T-cell subgroup data were collected for statistical analysis. TB-IGRA results were in positive proportion to the lymphocytes, CD4 + T cells and CD4 + CD28 + T cells, whereas negative to the Treg cells. Patient with unilateral pulmonary lesion had higher TB-IGRA than those with bilateral pulmonary lesions. After the stimulation of TB-specific antigen, the proportion of CD4 + IFN-γ + and CD8 + IFN-γ + T Tcells were both increased and the CD4 + IFN-γ + T had positive correlation with the value of TB-IGRA. IFN-γ was tested with TB-IGRA in patients with TB by the specific TB T cells and correlated with the lymphocytes, while the lymphocytes also closely related to the host's anti-TB immunity and disease outcome. Hence the result of TB-IGRA could reflect the specific anti-TB immunity ability of the host, disease progression and prognosis. This study further expands the application scope of TB-IGRA technology in the diagnosis of TB and lays a foundation for clinical practice to understand the immunity state of the patients with TB and the application of auxiliary clinical immunity regulators. © 2017 Wiley Periodicals, Inc.

Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences.

PubMed

Chattaway, Marie A; Schaefer, Ulf; Tewolde, Rediat; Dallman, Timothy J; Jenkins, Claire

2017-02-01

Escherichia coli and Shigella species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of Shigella are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982 Escherichia coli and Shigella sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive E. coli isolates that were misidentified as Shigella flexneri or S. boydii by the kmer ID, and 8 were S. flexneri isolates misidentified by TB&S as S. boydii due to nonfunctional S. flexneri O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both S. boydii and S. dysenteriae strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data. Shigella can be differentiated from E. coli and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of Shigella, and identified emerging pathoadapted lineages. © Crown copyright 2017.

Effectiveness of TB sensitization initiatives in improving the involvement of self help group members in rural TB control in south India.

PubMed

Thomas, Beena; Priscilla Rebecca, B; Dhanalakshmi, A; Rani, S; Deepa Lakshmi, A; Watson, Basilea; Vijayalakshmi, R; Muniyandi, M; Karikalan, N

2016-12-01

The 'End TB strategy' has highlighted the importance of inter-sectoral collaboration and community mobilization for achieving zero TB deaths by 2020. The aim of the study was to develop and test a model TB sensitization programme involving self help groups (SHGs). This experimental study was conducted in two blocks (intervention and control), in Tiruvallur district. The intervention content included short-lecture, musical story telling activity, role play, short film on TB. The impact was compared at baseline, third and sixth months in terms of SHGs' awareness, promotion of awareness, identification and referral of presumptive TB cases and provision of TB treatment. A total of 764 vs 796 SHGs were enrolled in control and intervention groups, respectively. The knowledge attitude, and practice score (lower score indicated a better attitude and practice), from baseline to 6 months was significantly reduced (29 to 24) in the intervention group. Similarly, a significant difference was observed in identification and referral of chest symptomatics in the intervention group at 3 and 6 months. During the 3 month follow-up a significantly higher proportion of SHG members were involved in TB awareness activities in the intervention (623/748 [83.3%]) vs control group (471/728 [64.7%]; p<0.001). Findings from this study highlight the feasibility of involving SHGs through a model TB sensitization program for strengthening TB prevention and control activities. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Whole genome sequencing of clinical strains of Mycobacterium tuberculosis from Mumbai, India: A potential tool for determining drug-resistance and strain lineage.

PubMed

Chatterjee, Anirvan; Nilgiriwala, Kayzad; Saranath, Dhananjaya; Rodrigues, Camilla; Mistry, Nerges

2017-12-01

Amplification of drug resistance in Mycobacterium tuberculosis (M.tb) and its transmission are significant barriers in controlling tuberculosis (TB) globally. Diagnostic inaccuracies and delays impede appropriate drug administration, which exacerbates primary and secondary drug resistance. Increasing affordability of whole genome sequencing (WGS) and exhaustive cataloguing of drug resistance mutations is poised to revolutionise TB diagnostics and facilitate personalized drug therapy. However, application of WGS for diagnostics in high endemic areas is yet to be demonstrated. We report WGS of 74 clinical TB isolates from Mumbai, India, characterising genotypic drug resistance to first- and second-line anti-TB drugs. A concordance analysis between phenotypic and genotypic drug susceptibility of a subset of 29 isolates and the sensitivity of resistance prediction to the 4 drugs was calculated, viz. isoniazid-100%, rifampicin-100%, ethambutol-100% and streptomycin-85%. The whole genome based phylogeny showed almost equal proportion of East Asian (27/74) and Central Asian (25/74) strains. Interestingly we also found a clonal group of 9 isolates, of which 7 patients were found to be from the same geographical location and accessed the same health post. This provides the first evidence of epidemiological linkage for tracking TB transmission in India, an approach which has the potential to significantly improve chances of End-TB goals. Finally, the use of Mykrobe Predictor, as a standalone drug resistance and strain typing tool, requiring just few minutes to analyse raw WGS data into tabulated results, implies the rapid clinical applicability of WGS based TB diagnosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strongly Circularly Polarized Emission from Water-Soluble Eu(III)- and Tb(III)-Based Complexes: A Structural and Spectroscopic Study.

PubMed

Leonzio, Marco; Melchior, Andrea; Faura, Georgina; Tolazzi, Marilena; Zinna, Francesco; Di Bari, Lorenzo; Piccinelli, Fabio

2017-04-17

Water-soluble Eu(III) and Tb(III) complexes with N,N'-bis(2-pyridylmethyl)-trans-1,2-diaminocyclohexane-N,N'-diacetic acid (H 2 bpcd) have been synthesized and characterized in their racemic and enantiopure forms. The ligand has been designed to bind Ln(III) ions, providing a dissymmetric environment able to solicit strong chiroptical features while at the same time leaving a few coordination sites available for engaging further ancillary ligands. Potentiometric studies show that Ln(III) complexes have a relatively good stability and that at pH 7 the [Ln(bpcd)] + species is largely dominant. DFT calculations carried out on the (S,S)-[Y(bpcd)(H 2 O) 5 ] + complexes (the closed-shell equivalents of [Eu(bpcd)(H 2 O) 5 ] + and [Tb(bpcd)(H 2 O) 5 ] + ) indicate that the two trans-O,O and trans-N py ,N py configurations are equally stable in solution and present two coordinated water molecules. This is in agreement with the hydration number ∼2.6 determined by luminescence lifetime measurements on Tb(III) and Eu(III) complexes. A detailed optical and chiroptical spectroscopic characterization has been carried out and reveals that the complexes display an efficient luminescence in the visible spectral range accompanied by a strong CPL activity. A value for g lum (around 0.1 on the top of the 546 nm band) for the Tb-based complex has been found. This is one of the highest g lum values measured up to now for chiral Tb complexes. These results suggest that in principle Tb(bpcd)Cl is suitable to be employed as a CPL bioprobe for relevant analytes in aqueous media.

Anomalous magnetoelastic behaviour near morphotropic phase boundary in ferromagnetic Tb 1-xNd xCo 2 system

DOE PAGES

Murtaza, Adil; Yang, Sen; Zhou, Chao; ...

2016-08-04

In this study, we report a morphotropic phase boundary (MPB) involved ferromagnetic system Tb 1-xNd xCo 2 and reveal the corresponding structural and magnetoelastic properties of this system. With high resolution synchrotron X-ray diffractometry, the crystal structure of the TbCo 2-rich side is detected to be rhombohedral and that of NdCo 2-rich side is tetragonal below their respective Curie temperatures TC. The MPB composition Tb 0.35Nd 0.65Co 2 corresponds to the coexistence of the rhombohedral phase (R-phase) and tetragonal phase ( T-phase). Contrary to previously reported MPB involved ferromagnetic systems, the MPB composition of Tb 0.35Nd 0.65Co 2 shows minimummore » magnetization which can be understood as compensation of sublattice moments between the R-phase and the T-phase. Furthermore, magnetostriction of Tb 1-xNd xCo 2 decreases with increasing Nd concentration until x = 0.8 and then increases in the negative direction with further increasing Nd concentration; the optimum point for magnetoelastic properties lies towards the rhombohedral phase. Finally, our work not only shows an anomalous type of ferromagnetic MPB but also provides an effective way to design functional materials.« less

Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates.

PubMed

Lasserre, Moira; Fresia, Pablo; Greif, Gonzalo; Iraola, Gregorio; Castro-Ramos, Miguel; Juambeltz, Arturo; Nuñez, Álvaro; Naya, Hugo; Robello, Carlos; Berná, Luisa

2018-01-02

Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%). Indeed, this characteristic is of major concern for correct typing and determination of strain-specific traits based on sequence diversity. Due to its historical economic dependence on cattle production, Uruguay is deeply affected by the prevailing incidence of Mycobacterium bovis. With the world's highest number of cattle per human, and its intensive cattle production, Uruguay represents a particularly suited setting to evaluate genomic variability among isolates, and the diversity traits associated to this pathogen. We compared 186 genomes from MTBC strains isolated worldwide, and found a highly structured population in M. bovis. The analysis of 23 new M. bovis genomes, belonging to strains isolated in Uruguay evidenced three groups present in the country. Despite presenting an expected highly conserved genomic structure and sequence, these strains segregate into a clustered manner within the worldwide phylogeny. Analysis of the non-pe/ppe differential areas against a reference genome defined four main sources of variability, namely: regions of difference (RD), variable genes, duplications and novel genes. RDs and variant analysis segregated the strains into clusters that are concordant with their spoligotype identities. Due to its high homoplasy rate, spoligotyping failed to reflect the true genomic diversity among worldwide representative strains, however, it remains a good indicator for closely related populations. This study introduces a comprehensive population structure analysis of worldwide M. bovis isolates. The incorporation and analysis of 23 novel Uruguayan M. bovis genomes, sheds light onto the genomic diversity of this

Enthalpy of Mixing in Al–Tb Liquid

DOE PAGES

Zhou, Shihuai; Tackes, Carl; Napolitano, Ralph

2017-06-21

The liquid-phase enthalpy of mixing for Al$-$Tb alloys is measured for 3, 5, 8, 10, and 20 at% Tb at selected temperatures in the range from 1364 to 1439 K. Methods include isothermal solution calorimetry and isoperibolic electromagnetic levitation drop calorimetry. Mixing enthalpy is determined relative to the unmixed pure (Al and Tb) components. The required formation enthalpy for the Al3Tb phase is computed from first-principles calculations. Finally, based on our measurements, three different semi-empirical solution models are offered for the excess free energy of the liquid, including regular, subregular, and associate model formulations. These models are also compared withmore » the Miedema model prediction of mixing enthalpy.« less

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

Coverage of whole proteome by structural genomics observed through protein homology modeling database

PubMed Central

Yamaguchi, Akihiro; Go, Mitiko

2006-01-01

We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics. PMID:17146617

High throughput platforms for structural genomics of integral membrane proteins.

PubMed

Mancia, Filippo; Love, James

2011-08-01

Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts. Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy. Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

PA-Tb-Cu MOF as luminescent nanoenzyme for catalytic assay of hydrogen peroxide.

PubMed

Qi, Zewan; Wang, Li; You, Qi; Chen, Yang

2017-10-15

Metal organic frameworks (MOFs) with flexible structures and components have aroused great interest in designing functional materials. In this work, we designed and made a kind of PA-Tb-Cu MOF nanoenzyme capable of emitting fluorescence for the catalytic reaction of hydrogen peroxide (H 2 O 2 ). Luminescent Tb 3+ , catalytic Cu 2+ and bridging ligand were assembled and integrated into a single material nanoenzyme. This PA-Tb-Cu MOF nanoenzyme not only possessed excellent catalytic activity comparable to horseradish peroxidase but also can real-time fluorescently indicate the concentration of H 2 O 2 as low as 0.2µM during catalysis. Luminescent PA-Tb-Cu MOF nanoenzyme did not need a common combined use of natural/artificial enzymes and chromogenic reactions for the quantification of H 2 O 2 in widely-used enzyme-catalytic reactions. The present strategy assembled directly from functional ions/molecules provides a new way for the design and development of smart, multifunctional artificial enzymes for wide applications in biocatalysis, bioassays and nano-biomedicine. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

PubMed Central

Cooper, Vaughn S.; Hatcher, Philip J.; Verheyde, Bart; Carlier, Aurélien; Vandamme, Peter

2017-01-01

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence. PMID:28430818

A comparative study on the luminescence properties of Ce3+/Tb3+ doped Gd-based host nanomaterials

NASA Astrophysics Data System (ADS)

Jadhao, Charushila Vasant; Rani, Barkha; Sahu, Niroj Kumar

2018-04-01

A comparative study on the crystal phases and their respective luminescence behaviour of Gd3+ based host materials such as GdPO4, GdF3, GdVO4 and Gd2O3 sensitized with 7at.% Ce3+ and activated with 5 at.% Tb3+ have been reported. The nanomaterials were prepared by polyol method using ethylene glycol as solvent and found to have different crystal structures such as monoclinic, orthorhombic, tetragonal and cubic phase. Clear characteristics emission from Tb3+ has been observed in all the samples when excited in the absorption wavelength of Ce3+ and Gd3+ (˜280 nm). Among all the above materials, intense emission of Tb3+ is found in GdPO4 followed by GdF3, Gd2O3 and GdVO4 respectively. The Tb3+ emission is strongly influenced by the energy transfer process and crystal structure of the host materials and hence this study will be important for choosing suitable materials for display devices and biomedical applications.

Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

USDA-ARS?s Scientific Manuscript database

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

Tracking and Treating Mobile Populations. The TB Net System. Migrant Clinicians Network Monograph Series. = El Sistema de Red para la TB.

ERIC Educational Resources Information Center

Migrant Clinicians Network, Inc., Austin, TX.

A comprehensive tracking and referral network that helps provide continuity of care for mobile populations with active tuberculosis (TB) or TB infection is considered essential for effective treatment of TB. However, the interstate referral system that exists between state health departments has been highly inefficient for serving migrant…

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

USDA-ARS?s Scientific Manuscript database

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identi...

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

PubMed

von Grotthuss, Marcin; Plewczynski, Dariusz; Ginalski, Krzysztof; Rychlewski, Leszek; Shakhnovich, Eugene I

2006-02-06

The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF.

Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep

PubMed Central

2010-01-01

Background The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (Ovis aries) to construct a linkage map for bighorn sheep, Ovis canadensis. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species. Results Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals. Conclusions We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the

Application Values of T-SPOT.TB in Clinical Rapid Diagnosis of Tuberculosis.

PubMed

Zhu, Feng; Ou, Qinfang; Zheng, Jian

2018-01-01

This paper aims to explore the application value of tuberculosis-specific enzyme-linked immunospot assay (T-SPOT.TB) in the diagnosis of tuberculosis. Fifty one patients with tuberculosis (TB) admitted to Wuxi No.5 People's Hospital, Wuxi, China from June 2015 to June 2017 were selected as the TB group, and 40 patients without tuberculosis admitted in the same period were randomly selected as the non-TB group. Patients in the two groups received T-SPOT.TB, TB antibody (TB-Ab) test and mycobacterium TB deoxyribonucleic acid (TB-DNA) test, and the results were compared. Comparisons of the sensitivity of the three methods showed that the sensitivity of T-SPOT.TB was the highest, followed by TB-DNA from sputum samples, and that of TB-Ab was the lowest. The specificity of TB-Ab was the highest, followed by T-SPOT.TB, and that of TB-DNA from sputum samples was the lowest. In the receiver operating characteristic (ROC) curve analysis, the area under curve (AUC) of T-SPOT.TB (0.896) was the highest, followed by TB-DNA from sputum samples (0.772), and that of sputum smears (0.698) was the lowest. T-SPOT.TB can quickly and accurately determine the presence of tuberculosis infection, and it is a non-invasive examination, which can further assist in the diagnosis and guide the treatment.

Antigen-Specific Interferon-Gamma Responses and Innate Cytokine Balance in TB-IRIS

PubMed Central

Goovaerts, Odin; Jennes, Wim; Massinga-Loembé, Marguerite; Ceulemans, Ann; Worodria, William; Mayanja-Kizza, Harriet; Colebunders, Robert; Kestens, Luc

2014-01-01

Background Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) remains a poorly understood complication in HIV-TB patients receiving antiretroviral therapy (ART). TB-IRIS could be associated with an exaggerated immune response to TB-antigens. We compared the recovery of IFNγ responses to recall and TB-antigens and explored in vitro innate cytokine production in TB-IRIS patients. Methods In a prospective cohort study of HIV-TB co-infected patients treated for TB before ART initiation, we compared 18 patients who developed TB-IRIS with 18 non-IRIS controls matched for age, sex and CD4 count. We analyzed IFNγ ELISpot responses to CMV, influenza, TB and LPS before ART and during TB-IRIS. CMV and LPS stimulated ELISpot supernatants were subsequently evaluated for production of IL-12p70, IL-6, TNFα and IL-10 by Luminex. Results Before ART, all responses were similar between TB-IRIS patients and non-IRIS controls. During TB-IRIS, IFNγ responses to TB and influenza antigens were comparable between TB-IRIS patients and non-IRIS controls, but responses to CMV and LPS remained significantly lower in TB-IRIS patients. Production of innate cytokines was similar between TB-IRIS patients and non-IRIS controls. However, upon LPS stimulation, IL-6/IL-10 and TNFα/IL-10 ratios were increased in TB-IRIS patients compared to non-IRIS controls. Conclusion TB-IRIS patients did not display excessive IFNγ responses to TB-antigens. In contrast, the reconstitution of CMV and LPS responses was delayed in the TB-IRIS group. For LPS, this was linked with a pro-inflammatory shift in the innate cytokine balance. These data are in support of a prominent role of the innate immune system in TB-IRIS. PMID:25415590

Effect of tuberculosis on the survival of HIV-infected men in a country with low TB incidence

PubMed Central

López-Gatell, H; Cole, SR; Margolick, JB; Witt, MD; Martinson, J; Phair, JP; Jacobson, LP

2010-01-01

Evidence regarding the effect of tuberculosis disease (TB) on HIV disease progression at the population level remains inconclusive. We estimated the effect of incident TB on time to acquired immunodeficiency syndrome (AIDS)-related death, using a marginal structural Cox model. Between 1984 and 2005, 2,882 HIV-infected men in the Multicenter AIDS Cohort Study contributed 21,914 person-years while followed for a median of 5.4 years. At study entry, the median CD4 cell count and HIV-1 RNA viral load were 533 cells/mm3 (interquartile range [IQR], 365 – 737) and 12,953 copies/ml (IQR, 2,453 – 48,540), respectively. This study was performed in a setting with a modest exposure to HAART; 8,295 of 23,801 (35%) person-years were followed during the HAART era. Fifteen men incurred incident TB, yielding a TB incidence of 7 (95% confidence interval [CI]: 4, 14) per 10,000 person-years, and 1,072 died of AIDS-related causes. Accounting for potential confounders, including CD4 cell count and viral load, the hazard of AIDS-related death was 2.4 times larger for the person-time with TB, compared to the person-time without TB (95% CI: 1.2, 4.7). Results underscore the importance of avoiding TB by using preventive interventions, such as treatment of latent TB infection, particularly in populations with a large prevalence of HIV/TB co-infected individuals. PMID:18753866

Interactive Exploration on Large Genomic Datasets.

PubMed

Tu, Eric

2016-01-01

The prevalence of large genomics datasets has made the the need to explore this data more important. Large sequencing projects like the 1000 Genomes Project [1], which reconstructed the genomes of 2,504 individuals sampled from 26 populations, have produced over 200TB of publically available data. Meanwhile, existing genomic visualization tools have been unable to scale with the growing amount of larger, more complex data. This difficulty is acute when viewing large regions (over 1 megabase, or 1,000,000 bases of DNA), or when concurrently viewing multiple samples of data. While genomic processing pipelines have shifted towards using distributed computing techniques, such as with ADAM [4], genomic visualization tools have not. In this work we present Mango, a scalable genome browser built on top of ADAM that can run both locally and on a cluster. Mango presents a combination of different optimizations that can be combined in a single application to drive novel genomic visualization techniques over terabytes of genomic data. By building visualization on top of a distributed processing pipeline, we can perform visualization queries over large regions that are not possible with current tools, and decrease the time for viewing large data sets. Mango is part of the Big Data Genomics project at University of California-Berkeley [25] and is published under the Apache 2 license. Mango is available at https://github.com/bigdatagenomics/mango.

A world of cities and the end of TB

PubMed Central

Prasad, Amit; Ross, Alex; Rosenberg, Paul; Dye, Christopher

2016-01-01

The WHO's End TB Strategy aims to reduce TB deaths by 95% and incidence by 90% between 2015 and 2035. As the world rapidly urbanizes, more people could have access to better infrastructure and services to help combat poverty and infectious diseases, including TB. And yet large numbers of people now live in overcrowded slums, with poor access to urban health services, amplifying the burden of TB. An alignment of the Sustainable Development Goals (SDGs) for health and for urban development provides an opportunity to accelerate the overall decline in infection and disease, and to create cities free of TB. PMID:26884491

Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory

PubMed Central

Crisan, Anamaria; McKee, Geoffrey; Munzner, Tamara

2018-01-01

Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics—including clinicians, laboratorians, epidemiologists, and researchers—is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results. Methods We used Design Study Methodology—a human centered approach drawn from the information visualization domain—to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report. Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design

Pastoralism and delay in diagnosis of TB in Ethiopia

PubMed Central

Gele, Abdi A; Bjune, Gunnar; Abebe, Fekadu

2009-01-01

Background Tuberculosis (TB) is a major public health problem in the Horn of Africa with Ethiopia being the most affected where TB cases increase at the rate of 2.6% each year. One of the main contributing factors for this rise is increasing transmission due to large number of untreated patients, serving as reservoirs of the infection within the communities. Reduction of the time between onset of TB symptoms to diagnosis is therefore a prerequisite to bring the TB epidemic under control. The aim of this study was to measure duration of delay among pastoralist TB patients at TB management units in Somali Regional State (SRS) of Ethiopia. Methods A cross sectional study of 226 TB patients with pastoralist identity was conducted in SRS of Ethiopia from June to September 2007. Patients were interviewed using questionnaire based interview. Time between onset of TB symptoms and first visit to a professional health care provider (patient delay), and the time between first visits to the professional health care provider to the date of diagnosis (medical provider's delay) were analyzed. Both pulmonary and extrapulmonary TB patients were included in the study. Result A total of 226 pastoralist TB patients were included in this study; 93 (41.2%) were nomadic pastoralists and 133 (58.8%) were agro-pastoralists. Median patient delay was found to be 60 days with range of 10–1800 days (83 days for nomadic pastoralists and 57 days for agro-pastoralists). Median health care provider's delay was 6 days and median total delay was 70 days in this study. Patient delay constituted 86% of the total delay. In multivariate logistic regression analysis, nomadic pastoralism (aOR. 2.69, CI 1.47–4.91) and having low biomedical knowledge on TB (aOR. 2.02, CI 1.02–3.98) were significantly associated with prolonged patient delay. However, the only observed risk factor for very long patient delay >120 days was distance to health facility (aOR.4.23, CI 1.32–13.54). Extra-pulmonary TB was

Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing.

PubMed

Parvaresh, Laila; Crighton, Taryn; Martinez, Elena; Bustamante, Andrea; Chen, Sharon; Sintchenko, Vitali

2018-06-07

The recurrence of tuberculosis (TB) disease in treated patients can serve as a marker of the efficacy of TB control programs. Recurrent disease represents either endogenous reactivation with the same strain of Mycobacterium tuberculosis due to non-compliance or inadequate therapy or exogenous reinfection with a new strain. Genotyping or whole genome sequencing (WGS) of M. tuberculosis isolates from initial and recurrent cases can differentiate between reinfection and reactivation. This study examined cases of recurrent TB in New South Wales, Australia, using genotyping and WGS. Culture-confirmed TB cases diagnosed at least 12 months apart between January 2011 and December 2016 were included. Isolates of M. tuberculosis from patients were compared using 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-24) typing and WGS. Eighteen cases of recurrent disease were identified but isolates from only 15 (83%) were available for study. MIRU-24 findings classified 13 (13/15; 87%) as reactivation and two (13%), as reinfection. Sequencing 13 cultivable paired isolates demonstrated 11 reactivations and two reinfections. There was genomic similarity in 10 out of 13 pairs while one case (1/13; 8%) had 12 SNPS differences. Two other cases (2/13;15%) had > 200 SNPs differences and were classified as reinfection. No phenotypic or genomic evidence of drug resistance was observed. TB control programs can achieve consistently low rates of recurrent disease in low incidence settings. WGS of implicated isolates augments the differentiation between reactivation and reinfection and indicates that the majority of recurrences are due to reactivation rather than reinfection. Predominance of reactivation over reinfection indicates high-quality public health practices and a low risk of local transmission. This study was approved by the Western Sydney Local Health District (WSLHD) Human Research Ethics Committee (HREC Ref: AU RED LNR/17/WMEAD/190; SSA

Report on cascade energy relaxation from PVP to Tb3+:Bi2SiO5 nanophosphor through salicylic acid in composite polymeric film

NASA Astrophysics Data System (ADS)

Kumari, Pushpa; Dwivedi, Y.

2018-05-01

The present article reports structural and spectroscopic properties of Tb:Bi2SiO5 nanophosphors dispersed in Polyvinylpyrrolidone polymer film, in presence of Salicylic acid (SA) molecule, which acts as a sensitizer. Detailed structural and spectroscopic characterizations were carried out using X-ray diffraction patterns, Scanning Electron Microscope, Fourier Transform Infrared and Excitation and photoluminescence techniques. The mean crystallite size of Tb3+:Bi2SiO5 nanophosphor and Tb3+:Bi2SiO5 in Polyvinylpyrrolidone polymer composite was estimated ∼22 nm and ∼28 nm, respectively. We have report atleast two times enhancement in Tb3+ ions emission intensity due to the efficient energy transfer from salicylic acid molecule to Tb ions. In addition to energy transfer from salicylic acid, the Polyvinylpyrrolidone polymeric host was also reported to serve as a sensitizer for SA molecule and Tb3+ ions through a cascade energy relaxation process while exciting with 248 nm photons. On 248 nm photon excitation, atleast five improvements in Tb3+ ion emission intensity are reported. Presence of SA molecule facilitates precise colour tuning as obvious from the CIE coordinates.

Utility of urine lipoarabinomannan (LAM) in diagnosing tuberculosis and predicting mortality with and without HIV: prospective TB cohort from the Thailand Big City TB Research Network.

PubMed

Suwanpimolkul, Gompol; Kawkitinarong, Kamon; Manosuthi, Weerawat; Sophonphan, Jiratchaya; Gatechompol, Sivaporn; Ohata, Pirapon June; Ubolyam, Sasiwimol; Iampornsin, Thatri; Katerattanakul, Pairaj; Avihingsanon, Anchalee; Ruxrungtham, Kiat

2017-06-01

To evaluate the applicability and accuracy of the urine lipoarabinomannan (LAM) test in tuberculosis (TB)/HIV co-infected patients and HIV-negative patients with disseminated TB. Frozen urine samples obtained at baseline from patients in the TB research cohort with proven culture-positive TB were selected for blinded urine LAM testing. One hundred and nine patients were categorized into four groups: (1) HIV-positive patients with TB; (2) HIV-negative patients with disseminated TB; (3) HIV-negative immunocompromised patients with TB; and (4) patients with diseases other than TB. The sensitivity of urine LAM testing for culture-positive TB, specificity of urine LAM testing for patients without TB, positive predictive value (PPV), and negative predictive value (NPV) were assessed. The sensitivity of the urine LAM test in group 1 patients with a CD4 T-cell count of >100, ≤100, and ≤50 cells/mm 3 was 38.5%, 40.6%, and 45%, respectively. The specificity and PPV of the urine LAM test were >80%. The sensitivity of the test was 20% in group 2 and 12.5% in group 3, and the specificity and PPV were 100% for both groups. A positive urine LAM test result was significantly associated with death. This promising diagnostic tool could increase the yield of TB diagnosis and may predict the mortality rate of TB infection, particularly in TB/HIV co-infected patients. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Extensively Drug-Resistant Tuberculosis (XDR TB)

MedlinePlus

... TB Reference Laboratory Network, the National TB Surveillance System in the United States, the national reference laboratory of South Korea, and ... capacity in the U.S. and abroad; and Developing education, risk, and media communications ... – United States, 1993–2006 CDC. CDC’s Role in Preventing XDR ...

Assessment of current practices in management of childhood TB among frontline clinicians in Southern Nigeria.

PubMed

Chukwu, Joseph N; Ukwaja, Kingsley N; Ekeke, Ngozi; Nwafor, Charles C; Meka, Anthony O; Madichie, Nelson O; Anyim, Moses C; Ogbudebe, Chidubem; Adegbesan, Julie; Ikebudu, Joy; Oshi, Daniel C

2016-07-01

Poor competence of clinicians may be a critical factor responsible for the under-diagnosis of childhood TB in high-burden settings. Our objective was to assess the current practices of management of childhood TB among clinicians in Nigeria. A cross-sectional survey was conducted among clinicians recruited through a three-stage sampling technique from 76 health facilities in Southern Nigeria. A semi-structured questionnaire was administered to all participants. Of 106 clinicians who completed the survey, 73 (68.9%) were <40 years and 67 (63.2%) were males. Also, 14 (13.2%) were paediatricians, 22 (20.8%) were paediatric specialist trainees and 70 (66%) were medical officers in primary and secondary care health facilities. About 94% of the respondents perceived diagnosis of childhood TB a challenge in Nigeria. The overall mean (SD) knowledge score was 3.8±0.9 (maximum 5), and 68 (64.2%) had good knowledge of childhood TB. The mean (SD) appropriate practice score was 4.0±1.7 (maximum 10) and, only 8 (7.5%) of them were considered to have adopted appropriate practices regarding childhood TB care. There are gaps in practices adopted by frontline clinicians in the management of childhood TB in Nigeria. Focused training of health workers on childhood TB care is urgently recommended. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Community-based MDR-TB care project improves treatment initiation in patients diagnosed with MDR-TB in Myanmar.

PubMed

Wai, Pyae Phyo; Shewade, Hemant Deepak; Kyaw, Nang Thu Thu; Thein, Saw; Si Thu, Aung; Kyaw, Khine Wut Yee; Aye, Nyein Nyein; Phyo, Aye Mon; Maung, Htet Myet Win; Soe, Kyaw Thu; Aung, Si Thu

2018-01-01

The Union in collaboration with national TB programme (NTP) started the community-based MDR-TB care (CBMDR-TBC) project in 33 townships of upper Myanmar to improve treatment initiation and treatment adherence. Patients with MDR-TB diagnosed/registered under NTP received support through the project staff, in addition to the routine domiciliary care provided by NTP staff. Each township had a project nurse exclusively for MDR-TB and 30 USD per month (max. for 4 months) were provided to the patient as a pre-treatment support. To assess whether CBMDR-TBC project's support improved treatment initiation. In this cohort study (involving record review) of all diagnosed MDR-TB between January 2015 and June 2016 in project townships, CBMDR-TBC status was categorized as "receiving support" if date of project initiation in patient's township was before the date of diagnosis and "not receiving support", if otherwise. Cox proportional hazards regression (censored on 31 Dec 2016) was done to identify predictors of treatment initiation. Of 456 patients, 57% initiated treatment: 64% and 56% among patients "receiving support (n = 208)" and "not receiving support (n = 228)" respectively (CBMDR-TBC status was not known in 20 (4%) patients due to missing diagnosis dates). Among those initiated on treatment (n = 261), median (IQR) time to initiate treatment was 38 (20, 76) days: 31 (18, 50) among patients "receiving support" and 50 (26,101) among patients "not receiving support". After adjusting other potential confounders (age, sex, region, HIV, past history of TB treatment), patients "receiving support" had 80% higher chance of initiating treatment [aHR (0.95 CI): 1.8 (1.3, 2.3)] when compared to patients "not receiving support". In addition, age 15-54 years, previous history of TB and being HIV negative were independent predictors of treatment initiation. Receiving support under CBMDR-TBC project improved treatment initiation: it not only improved the proportion initiated but also

Investigation of mitochondrial sequence variants associated with aminoglycoside-induced ototoxicity in South African TB patients on aminoglycosides.

PubMed

Human, Hanniqué; Hagen, Christian M; de Jong, Greetje; Harris, Tashneem; Lombard, Debbie; Christiansen, Michael; Bardien, Soraya

2010-03-19

A known side effect of aminoglycoside antibiotics is the development of permanent hearing loss. As South Africa is currently facing a tuberculosis (TB) epidemic, with an increasing number of multi-drug resistant tuberculosis (MDR-TB) infections, the use of aminoglycosides is on the increase. It is therefore important to determine whether the mitochondrial mutations associated with aminoglycoside-induced hearing loss occur at high frequencies in particular ethnic groups in our population. A total of 115 mainly MDR-TB patients all on aminoglycosides and 439 controls representative of the main ethnic groups in South Africa were screened for six mutations using the SNaPshot technique. Furthermore, the mitochondrial genomes of eight patients with ototoxicity were sequenced. Homoplasmic mutations were found in controls (A1555G in 0.9% of Black controls and A827G in 1.1% of Afrikaner controls) which reveal that a significant proportion of the South African population is genetically predisposed to developing aminoglycoside-induced hearing loss. The 961 delT+insC((n)) and T961G variants were found at frequencies of >1% indicating that both are probably non-pathogenic polymorphisms. Sequencing of the entire mitochondrial genome in eight patients did not reveal any mutations in the MT-RNR1 gene. However, two potentially pathogenic variants, T10114C (I19T in MT-ND3) and T15312C (I189T in MT-CYB) were found that may impact on the oxidative phosphorylation capacity and warrant further investigation for their possible role in this disorder. It is imperative that the genetic basis of this potentially preventable condition be investigated, particularly in countries where aminoglycosides are still commonly used, in order to identify individuals and/or ethnic groups who are at risk for this type of hearing loss. Copyright 2010 Elsevier Inc. All rights reserved.

Addressing diabetes mellitus as part of the strategy for ending TB

PubMed Central

Harries, Anthony D.; Kumar, Ajay M.V.; Satyanarayana, Srinath; Lin, Yan; Zachariah, Rony; Lönnroth, Knut; Kapur, Anil

2016-01-01

As we enter the new era of Sustainable Development Goals, the international community has committed to ending the TB epidemic by 2030 through implementation of an ambitious strategy to reduce TB-incidence and TB-related mortality and avoiding catastrophic costs for TB-affected families. Diabetes mellitus (DM) triples the risk of TB and increases the probability of adverse TB treatment outcomes such as failure, death and recurrent TB. The rapidly escalating global epidemic of DM means that DM needs to be addressed if TB-related milestones and targets are to be achieved. WHO and the International Union Against Tuberculosis and Lung Disease's Collaborative Framework for Care and Control of Tuberculosis and Diabetes, launched in 2011, provides a template to guide policy makers and implementers to combat the epidemics of both diseases. However, more evidence is required to answer important questions about bi-directional screening, optimal ways of delivering treatment, integration of DM and TB services, and infection control. This should in turn contribute to better and earlier TB case detection, and improved TB treatment outcomes and prevention. DM and TB collaborative care can also help guide the development of a more effective and integrated public health approach for managing non-communicable diseases. PMID:26884497

TB questions, East Kwaio answers: community-based participatory research in a remote area of Solomon Islands.

PubMed

Massey, P D; Wakageni, J; Kekeubata, E; Maena'adi, J; Laete'esafi, J; Waneagea, J; Fangaria, G; Jimuru, C; Houaimane, M; Talana, J; MacLaren, D; Speare, R

2012-01-01

East Kwaio is a remote region on the island of Malaita, Solomon Islands. Atoifi Adventist Hospital (the Hospital) is the only hospital and tuberculosis (TB) services provider in the region. If people come to the Hospital with TB, they are usually admitted for the two-month intensive phase of treatment as there are no community-based TB services. Most people walk or travel by canoe to the Hospital as there are no roads. East Kwaio is known to have high rates of TB; however, it has a low case detection rate and low treatment completion. The aims of this study were to explore why people with TB, especially from the mountain areas, present to the Hospital so late in their illness or do not present at all. The study was part of a larger project to strengthen the research capacity of local health workers and community leaders, supported by visiting researchers from Australia. Semi-structured interviews with TB patients, a focus group of key informants and direct interaction with a community with a history of TB were used to explore reasons why people present to the Hospital late in their TB illness. Four interviews and a focus group of 12 key informants were conducted and a mountain hamlet with a history of TB was visited. The results represent the data from the interviews and the focus group. The time delay in presenting to the Hospital from when participants first became unwell ranged between two and three years. In the mountain hamlet, two additional people with probable TB were seen who had not presented to the Hospital during illnesses of five and nine months. Reasons for delays included: seeking care from traditional healers; the challenge of accessing health services due to distance, cost and cultural issues different from the Hospital's worldview; social isolation when in hospital; and being old so not having long to live. Delays in diagnosis of people with TB will increase the risk of transmission to family and through hamlets and villages. This study has led to

Towards fully automated structure-based function prediction in structural genomics: a case study.

PubMed

Watson, James D; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A; Thornton, Janet M

2007-04-13

As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.

Effect of glycemic control and type of diabetes treatment on unsuccessful TB treatment outcomes among people with TB-Diabetes: A systematic review

PubMed Central

Jeyashree, Kathiresan; Mahajan, Preetam; Shah, Amar N.; Kirubakaran, Richard; Rao, Raghuram; Kumar, Ajay M. V.

2017-01-01

Background Stringent glycemic control by using insulin as a replacement or in addition to oral hypoglycemic agents (OHAs) has been recommended for people with tuberculosis and diabetes mellitus (TB-DM). This systematic review (PROSPERO 2016:CRD42016039101) analyses whether this improves TB treatment outcomes. Objectives Among people with drug-susceptible TB and DM on anti-TB treatment, to determine the effect of i) glycemic control (stringent or less stringent) compared to poor glycemic control and ii) insulin (only or with OHAs) compared to ‘OHAs only’ on unsuccessful TB treatment outcome(s). We looked for unfavourable TB treatment outcomes at the end of intensive phase and/or end of TB treatment (minimum six months and maximum 12 months follow up). Secondary outcomes were development of MDR-TB during the course of treatment, recurrence after 6 months and/or after 1 year post successful treatment completion and development of adverse events related to glucose lowering treatment (including hypoglycemic episodes). Methods All interventional studies (with comparison arm) and cohort studies on people with TB-DM on anti-TB treatment reporting glycemic control, DM treatment details and TB treatment outcomes were eligible. We searched electronic databases (EMBASE, PubMed, Google Scholar) and grey literature between 1996 and April 2017. Screening, data extraction and risk of bias assessment were done independently by two investigators and recourse to a third investigator, for resolution of differences. Results After removal of duplicates from 2326 identified articles, 2054 underwent title and abstract screening. Following full text screening of 56 articles, nine cohort studies were included. Considering high methodological and clinical heterogeneity, we decided to report the results qualitatively and not perform a meta-analysis. Eight studies dealt with glycemic control, of which only two were free of the risk of bias (with confounder-adjusted measures of effect). An

Effect of glycemic control and type of diabetes treatment on unsuccessful TB treatment outcomes among people with TB-Diabetes: A systematic review.

PubMed

Shewade, Hemant Deepak; Jeyashree, Kathiresan; Mahajan, Preetam; Shah, Amar N; Kirubakaran, Richard; Rao, Raghuram; Kumar, Ajay M V

2017-01-01

Stringent glycemic control by using insulin as a replacement or in addition to oral hypoglycemic agents (OHAs) has been recommended for people with tuberculosis and diabetes mellitus (TB-DM). This systematic review (PROSPERO 2016:CRD42016039101) analyses whether this improves TB treatment outcomes. Among people with drug-susceptible TB and DM on anti-TB treatment, to determine the effect of i) glycemic control (stringent or less stringent) compared to poor glycemic control and ii) insulin (only or with OHAs) compared to 'OHAs only' on unsuccessful TB treatment outcome(s). We looked for unfavourable TB treatment outcomes at the end of intensive phase and/or end of TB treatment (minimum six months and maximum 12 months follow up). Secondary outcomes were development of MDR-TB during the course of treatment, recurrence after 6 months and/or after 1 year post successful treatment completion and development of adverse events related to glucose lowering treatment (including hypoglycemic episodes). All interventional studies (with comparison arm) and cohort studies on people with TB-DM on anti-TB treatment reporting glycemic control, DM treatment details and TB treatment outcomes were eligible. We searched electronic databases (EMBASE, PubMed, Google Scholar) and grey literature between 1996 and April 2017. Screening, data extraction and risk of bias assessment were done independently by two investigators and recourse to a third investigator, for resolution of differences. After removal of duplicates from 2326 identified articles, 2054 underwent title and abstract screening. Following full text screening of 56 articles, nine cohort studies were included. Considering high methodological and clinical heterogeneity, we decided to report the results qualitatively and not perform a meta-analysis. Eight studies dealt with glycemic control, of which only two were free of the risk of bias (with confounder-adjusted measures of effect). An Indian study reported 30% fewer

An integrated map of structural variation in 2,504 human genomes.

PubMed

Sudmant, Peter H; Rausch, Tobias; Gardner, Eugene J; Handsaker, Robert E; Abyzov, Alexej; Huddleston, John; Zhang, Yan; Ye, Kai; Jun, Goo; Fritz, Markus Hsi-Yang; Konkel, Miriam K; Malhotra, Ankit; Stütz, Adrian M; Shi, Xinghua; Casale, Francesco Paolo; Chen, Jieming; Hormozdiari, Fereydoun; Dayama, Gargi; Chen, Ken; Malig, Maika; Chaisson, Mark J P; Walter, Klaudia; Meiers, Sascha; Kashin, Seva; Garrison, Erik; Auton, Adam; Lam, Hugo Y K; Mu, Xinmeng Jasmine; Alkan, Can; Antaki, Danny; Bae, Taejeong; Cerveira, Eliza; Chines, Peter; Chong, Zechen; Clarke, Laura; Dal, Elif; Ding, Li; Emery, Sarah; Fan, Xian; Gujral, Madhusudan; Kahveci, Fatma; Kidd, Jeffrey M; Kong, Yu; Lameijer, Eric-Wubbo; McCarthy, Shane; Flicek, Paul; Gibbs, Richard A; Marth, Gabor; Mason, Christopher E; Menelaou, Androniki; Muzny, Donna M; Nelson, Bradley J; Noor, Amina; Parrish, Nicholas F; Pendleton, Matthew; Quitadamo, Andrew; Raeder, Benjamin; Schadt, Eric E; Romanovitch, Mallory; Schlattl, Andreas; Sebra, Robert; Shabalin, Andrey A; Untergasser, Andreas; Walker, Jerilyn A; Wang, Min; Yu, Fuli; Zhang, Chengsheng; Zhang, Jing; Zheng-Bradley, Xiangqun; Zhou, Wanding; Zichner, Thomas; Sebat, Jonathan; Batzer, Mark A; McCarroll, Steven A; Mills, Ryan E; Gerstein, Mark B; Bashir, Ali; Stegle, Oliver; Devine, Scott E; Lee, Charles; Eichler, Evan E; Korbel, Jan O

2015-10-01

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋ xTb xVO₃ (x=0 and 0.2)

DOE PAGES

Yan, J.-Q.; Cao, H. B.; McGuire, M. A.; ...

2013-06-10

The spin and orbital ordering in Dy₁₋ xTb xVO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy 0.8Tb 0.20VO 3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dymore » sublattice by external magnetic fields couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋ xTb xVO₃.« less

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

PubMed

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

On the Structural Plasticity of the Human Genome: Chromosomal Inversions Revisited

PubMed Central

Alves, Joao M; Lopes, Alexandra M; Chikhi, Lounès; Amorim, António

2012-01-01

With the aid of novel and powerful molecular biology techniques, recent years have witnessed a dramatic increase in the number of studies reporting the involvement of complex structural variants in several genomic disorders. In fact, with the discovery of Copy Number Variants (CNVs) and other forms of unbalanced structural variation, much attention has been directed to the detection and characterization of such rearrangements, as well as the identification of the mechanisms involved in their formation. However, it has long been appreciated that chromosomes can undergo other forms of structural changes - balanced rearrangements - that do not involve quantitative variation of genetic material. Indeed, a particular subtype of balanced rearrangement – inversions – was recently found to be far more common than had been predicted from traditional cytogenetics. Chromosomal inversions alter the orientation of a specific genomic sequence and, unless involving breaks in coding or regulatory regions (and, disregarding complex trans effects, in their close vicinity), appear to be phenotypically silent. Such a surprising finding, which is difficult to reconcile with the classical interpretation of inversions as a mechanism causing subfertility (and ultimately reproductive isolation), motivated a new series of theoretical and empirical studies dedicated to understand their role in human genome evolution and to explore their possible association to complex genetic disorders. With this review, we attempt to describe the latest methodological improvements to inversions detection at a genome wide level, while exploring some of the possible implications of inversion rearrangements on the evolution of the human genome. PMID:23730202

A world of cities and the end of TB.

PubMed

Prasad, Amit; Ross, Alex; Rosenberg, Paul; Dye, Christopher

2016-03-01

The WHO's End TB Strategy aims to reduce TB deaths by 95% and incidence by 90% between 2015 and 2035. As the world rapidly urbanizes, more people could have access to better infrastructure and services to help combat poverty and infectious diseases, including TB. And yet large numbers of people now live in overcrowded slums, with poor access to urban health services, amplifying the burden of TB. An alignment of the Sustainable Development Goals (SDGs) for health and for urban development provides an opportunity to accelerate the overall decline in infection and disease, and to create cities free of TB. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

Tuberculosis (TB): Treatment

MedlinePlus

... Education & Training Home Conditions Tuberculosis (TB) Tuberculosis: Treatment Tuberculosis: Treatment Make an Appointment Refer a Patient Ask ... or bones is treated longer. NEXT: Preventive Treatment Tuberculosis: Diagnosis Tuberculosis: History Clinical Trials For more than ...

Migration, TB control and elimination: Whom to screen and treat.

PubMed

Rendon, A; Centis, R; Zellweger, J-P; Solovic, I; Torres-Duque, C A; Robalo Cordeiro, C; de Queiroz Mello, F C; Manissero, D; Sotgiu, G

Tuberculosis (TB) in migrants represents an important clinical and public health threat, particularly in low TB incidence countries. The current review is aimed to assess issues related to screening and treatment of migrants with latent TB infection or TB disease. Copyright © 2017 Sociedade Portuguesa de Pneumologia. Published by Elsevier España, S.L.U. All rights reserved.

Direct two-photon excitation of Sm3+, Eu3+, Tb3+, Tb.DOTA-, and Tb.propargylDO3A in solution

NASA Astrophysics Data System (ADS)

Sørensen, Thomas Just; Blackburn, Octavia A.; Tropiano, Manuel; Faulkner, Stephen

2012-07-01

We have observed direct two-photon excitation of samarium, europium and terbium ions in solution upon near IR excitation using a tuneable pulsed light source, and have also studied two-photon processes in a pair of related terbium complexes, namely [Tb.DOTA]- and Tb.propargylDO3A. Direct two-photon excitation of lanthanides is observed in simple systems in the absence of sensitizing chromophores. Where even simple chromophores such as a triple bond are present in the complex, then single and two-photon excitation of chromophore excited states competes with direct two-photon excitation of the ions and is the dominant pathway for sensitizing formation of the lanthanide excited state.

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.

PubMed

Li, Sanshu; Breaker, Ronald R

2017-10-13

With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies. We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements. Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs

Are We Doing Enough to Stem the Tide of Acquired MDR-TB in Countries with High TB Burden? Results of a Mixed Method Study in Chongqing, China

PubMed Central

Li, Ying; Ehiri, John; Oren, Eyal; Hu, Daiyu; Luo, Xingneng; Liu, Ying; Li, Daikun; Wang, Qingya

2014-01-01

Multi-drug resistant tuberculosis (MDR-TB) represents a threat to health and development in countries with high TB burden. China’s MDR-TB prevalence rate of 6.8% is the highest in the world. Interventions to remove barriers against effective TB control, and prevention of MDR-TB are urgently needed in the country. This paper reports a cross-sectional questionnaire survey of 513 pulmonary TB (PTB) patients, and qualitative interviews of 10 healthcare workers (HCWs), and 15 PTB patients. The objective was to assess barriers against effective control of PTB and prevention of MDR-TB by elucidating the perspectives of patients and healthcare providers. Results showed that more than half of the patients experienced patient delay of over 12.5 days. A similar proportion also experienced detection delay of over 30 days, and delay in initiating treatment of over 31 days. Consulting a non-TB health facility ≥3 times before seeking care at TB dispensary was a risk factor for both detection delay [AOR (95% CI): 1.89(1.07, 3.34) and delay in initiating treatment[AOR (95% CI): 1.88 (1.06, 3.36). Results revealed poor implementation of Directly Observed Therapy (DOT), whereby treatment of 34.3% patients was never monitored by HCWs. Only 31.8% patients had ever accessed TB health education before their TB diagnosis. Qualitative data consistently disclosed long patient delay, and indicated that patient’s poor TB knowledge and socioeconomic barriers were primary reasons for patient delay. Seeking care and being treated at a non-TB hospital was an important reason for detection delay. Patient’s long work hours and low income increased risk for treatment non-adherence. Evidence-based measures to improve TB health seeking behavior, reduce patient and detection delays, improve the quality of DOT, address financial and system barriers, and increase access to TB health promotion are urgently needed to address the burgeoning prevalence of MDR-TB in China. PMID:24505476

Investigation on optical band gap, photoluminescence properties and concentration quenching mechanism of Pb1-x Tb3+xWO4 green-emitting phosphors.

PubMed

Chanu, Thokchom Taru Taru; Rajmuhon Singh, N

2018-02-15

A series of monophasic Tb 3+ (2, 5, 7, 10 and 15at%) doped PbWO 4 phosphors were successfully prepared via hydrothermal method. X-ray diffraction patterns revealed that the prepared samples possess a high crystallinity with tetragonal scheelite-type structure. FT-IR and Raman analysis exhibited a WO stretching peak of WO 4 2- group, which is also related to the scheelite structure. UV-visible diffuse reflectance spectra indicated a reduction in the optical band gap with the replacement of Pb 2+ by Tb 3+ ions. The presence of strong and intense emission peaks characteristic of Tb 3+ with the dominant peak at 545nm (green, 5 D 4 → 7 F 5 transition) under UV irradiation at 320nm demonstrated an efficient energy transfer from the host to Tb 3+ ions. Using Van Uitert's model, the concentration quenching mechanism between Tb 3+ ions in PbWO 4 :Tb 3+ phosphor was attributed to a dipole-dipole interaction and the critical distance was determined to be ~12Å. The decay lifetimes and CIE chromaticity co-ordinates of PbWO 4 :Tb 3+ phosphors were also investigated in detail. These prepared materials might serve as a potential phosphor for LED applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation on optical band gap, photoluminescence properties and concentration quenching mechanism of Pb1 - x Tb3 +xWO4 green-emitting phosphors

NASA Astrophysics Data System (ADS)

Chanu, Thokchom Taru Taru; Rajmuhon Singh, N.

2018-02-01

A series of monophasic Tb3 + (2, 5, 7, 10 and 15 at%) doped PbWO4 phosphors were successfully prepared via hydrothermal method. X-ray diffraction patterns revealed that the prepared samples possess a high crystallinity with tetragonal scheelite-type structure. FT-IR and Raman analysis exhibited a Wsbnd O stretching peak of WO42 - group, which is also related to the scheelite structure. UV-visible diffuse reflectance spectra indicated a reduction in the optical band gap with the replacement of Pb2 + by Tb3 + ions. The presence of strong and intense emission peaks characteristic of Tb3 + with the dominant peak at 545 nm (green, 5D4 → 7F5 transition) under UV irradiation at 320 nm demonstrated an efficient energy transfer from the host to Tb3 + ions. Using Van Uitert's model, the concentration quenching mechanism between Tb3 + ions in PbWO4:Tb3 + phosphor was attributed to a dipole-dipole interaction and the critical distance was determined to be 12 Å. The decay lifetimes and CIE chromaticity co-ordinates of PbWO4:Tb3 + phosphors were also investigated in detail. These prepared materials might serve as a potential phosphor for LED applications.

Catching the missing million: experiences in enhancing TB & DR-TB detection by providing upfront Xpert MTB/RIF testing for people living with HIV in India.

PubMed

Raizada, Neeraj; Sachdeva, Kuldeep Singh; Sreenivas, Achuthan; Kulsange, Shubhangi; Gupta, Radhey Shyam; Thakur, Rahul; Dewan, Puneet; Boehme, Catharina; Paramsivan, Chinnambedu Nainarappan

2015-01-01

A critical challenge in providing TB care to People Living with HIV (PLHIV) is establishing an accurate bacteriological diagnosis. Xpert MTB/RIF, a highly sensitive and specific rapid tool, offers a promising solution in addressing these challenges. This study presents results from PLHIV taking part in a large demonstration study across India wherein upfront Xpert MTB/RIF testing was offered to all presumptive PTB cases in public health facilities. The study covered a population of 8.8 million across 18 sub-district level tuberculosis units (TU), with one Xpert MTB/RIF platform established at each TU. All HIV-infected patients suspected of TB (both TB and Drug Resistant TB (DR-TB)) accessing public health facilities in study area were prospectively enrolled and provided upfront Xpert MTB/RIF testing. 2,787 HIV-infected presumptive pulmonary TB cases were enrolled and 867 (31.1%, 95% Confidence Interval (CI) 29.4‒32.8) HIV-infected TB cases were diagnosed under the study. Overall 27.6% (CI 25.9-29.3) of HIV-infected presumptive PTB cases were positive by Xpert MTB/RIF, compared with 12.9% (CI 11.6-14.1) who had positive sputum smears. Upfront Xpert MTB/RIF testing of presumptive PTB and DR-TB cases resulted in diagnosis of 73 (9.5%, CI 7.6‒11.8) and 16 (11.2%, CI 6.7‒17.1) rifampicin resistance cases, respectively. Positive predictive value (PPV) for rifampicin resistance detection was high 97.7% (CI 89.3‒99.8), with no significant difference with or without prior history of TB treatment. The study results strongly demonstrate limitations of using smear microscopy for TB diagnosis in PLHIV, leading to low TB and DR-TB detection which can potentially lead to either delayed or sub-optimal TB treatment. Our findings demonstrate the usefulness and feasibility of addressing this diagnostic gap with upfront of Xpert MTB/RIF testing, leading to overall strengthening of care and support package for PLHIV.

Catching the Missing Million: Experiences in Enhancing TB & DR-TB Detection by Providing Upfront Xpert MTB/RIF Testing for People Living with HIV in India

PubMed Central

Raizada, Neeraj; Sachdeva, Kuldeep Singh; Sreenivas, Achuthan; Kulsange, Shubhangi; Gupta, Radhey Shyam; Thakur, Rahul; Dewan, Puneet; Boehme, Catharina; Paramsivan, Chinnambedu Nainarappan

2015-01-01

Background A critical challenge in providing TB care to People Living with HIV (PLHIV) is establishing an accurate bacteriological diagnosis. Xpert MTB/RIF, a highly sensitive and specific rapid tool, offers a promising solution in addressing these challenges. This study presents results from PLHIV taking part in a large demonstration study across India wherein upfront Xpert MTB/RIF testing was offered to all presumptive PTB cases in public health facilities. Method The study covered a population of 8.8 million across 18 sub-district level tuberculosis units (TU), with one Xpert MTB/RIF platform established at each TU. All HIV-infected patients suspected of TB (both TB and Drug Resistant TB (DR-TB)) accessing public health facilities in study area were prospectively enrolled and provided upfront Xpert MTB/RIF testing. Result 2,787 HIV-infected presumptive pulmonary TB cases were enrolled and 867 (31.1%, 95% Confidence Interval (CI) 29.4‒32.8) HIV-infected TB cases were diagnosed under the study. Overall 27.6% (CI 25.9–29.3) of HIV-infected presumptive PTB cases were positive by Xpert MTB/RIF, compared with 12.9% (CI 11.6–14.1) who had positive sputum smears. Upfront Xpert MTB/RIF testing of presumptive PTB and DR-TB cases resulted in diagnosis of 73 (9.5%, CI 7.6‒11.8) and 16 (11.2%, CI 6.7‒17.1) rifampicin resistance cases, respectively. Positive predictive value (PPV) for rifampicin resistance detection was high 97.7% (CI 89.3‒99.8), with no significant difference with or without prior history of TB treatment. Conclusion The study results strongly demonstrate limitations of using smear microscopy for TB diagnosis in PLHIV, leading to low TB and DR-TB detection which can potentially lead to either delayed or sub-optimal TB treatment. Our findings demonstrate the usefulness and feasibility of addressing this diagnostic gap with upfront of Xpert MTB/RIF testing, leading to overall strengthening of care and support package for PLHIV. PMID:25658091

TOPSAN: a dynamic web database for structural genomics.

PubMed

Ellrott, Kyle; Zmasek, Christian M; Weekes, Dana; Sri Krishna, S; Bakolitsa, Constantina; Godzik, Adam; Wooley, John

2011-01-01

The Open Protein Structure Annotation Network (TOPSAN) is a web-based collaboration platform for exploring and annotating structures determined by structural genomics efforts. Characterization of those structures presents a challenge since the majority of the proteins themselves have not yet been characterized. Responding to this challenge, the TOPSAN platform facilitates collaborative annotation and investigation via a user-friendly web-based interface pre-populated with automatically generated information. Semantic web technologies expand and enrich TOPSAN's content through links to larger sets of related databases, and thus, enable data integration from disparate sources and data mining via conventional query languages. TOPSAN can be found at http://www.topsan.org.

Analysis of multi drug resistant tuberculosis (MDR-TB) financial protection policy: MDR-TB health insurance schemes, in Chhattisgarh state, India.

PubMed

Kundu, Debashish; Sharma, Nandini; Chadha, Sarabjit; Laokri, Samia; Awungafac, George; Jiang, Lai; Asaria, Miqdad

2018-01-27

There are significant financial barriers to access treatment for multi drug resistant tuberculosis (MDR-TB) in India. To address these challenges, Chhattisgarh state in India has established a MDR-TB financial protection policy by creating MDR-TB benefit packages as part of the universal health insurance scheme that the state has rolled out in their effort towards attaining Universal Health Coverage for all its residents. In these schemes the state purchases health insurance against set packages of services from third party health insurance agencies on behalf of all its residents. Provider payment reform by strategic purchasing through output based payments (lump sum fee is reimbursed as per the MDR-TB benefit package rates) to the providers - both public and private health facilities empanelled under the insurance scheme was the key intervention. To understand the implementation gap between policy and practice of the benefit packages with respect to equity in utilization of package claims by the poor patients in public and private sector. Data from primary health insurance claims from January 2013 to December 2015, were analysed using an extension of 'Kingdon's multiple streams for policy implementation framework' to explain the implementation gap between policy and practice of the MDR-TB benefit packages. The total number of claims for MDR-TB benefit packages increased over the study period mainly from poor patients treated in public facilities, particularly for the pre-treatment evaluation and hospital stay packages. Variations and inequities in utilizing the packages were observed between poor and non-poor beneficiaries in public and private sector. Private providers participation in the new MDR-TB financial protection mechanism through the universal health insurance scheme was observed to be much lower than might be expected given their share of healthcare provision overall in India. Our findings suggest that there may be an implementation gap due to weak

Community-based MDR-TB care project improves treatment initiation in patients diagnosed with MDR-TB in Myanmar

PubMed Central

Shewade, Hemant Deepak; Kyaw, Nang Thu Thu; Thein, Saw; Si Thu, Aung; Kyaw, Khine Wut Yee; Aye, Nyein Nyein; Phyo, Aye Mon; Maung, Htet Myet Win; Soe, Kyaw Thu; Aung, Si Thu

2018-01-01

Background The Union in collaboration with national TB programme (NTP) started the community-based MDR-TB care (CBMDR-TBC) project in 33 townships of upper Myanmar to improve treatment initiation and treatment adherence. Patients with MDR-TB diagnosed/registered under NTP received support through the project staff, in addition to the routine domiciliary care provided by NTP staff. Each township had a project nurse exclusively for MDR-TB and 30 USD per month (max. for 4 months) were provided to the patient as a pre-treatment support. Objectives To assess whether CBMDR-TBC project’s support improved treatment initiation. Methods In this cohort study (involving record review) of all diagnosed MDR-TB between January 2015 and June 2016 in project townships, CBMDR-TBC status was categorized as “receiving support” if date of project initiation in patient’s township was before the date of diagnosis and “not receiving support”, if otherwise. Cox proportional hazards regression (censored on 31 Dec 2016) was done to identify predictors of treatment initiation. Results Of 456 patients, 57% initiated treatment: 64% and 56% among patients “receiving support (n = 208)” and “not receiving support (n = 228)” respectively (CBMDR-TBC status was not known in 20 (4%) patients due to missing diagnosis dates). Among those initiated on treatment (n = 261), median (IQR) time to initiate treatment was 38 (20, 76) days: 31 (18, 50) among patients “receiving support” and 50 (26,101) among patients “not receiving support”. After adjusting other potential confounders (age, sex, region, HIV, past history of TB treatment), patients “receiving support” had 80% higher chance of initiating treatment [aHR (0.95 CI): 1.8 (1.3, 2.3)] when compared to patients “not receiving support”. In addition, age 15–54 years, previous history of TB and being HIV negative were independent predictors of treatment initiation. Conclusion Receiving support under CBMDR-TBC project

Photoluminescence and energy transfer process in Gd{sub 2}O{sub 3}:Eu{sup 3+}, Tb{sup 3+}

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

Selvalakshmi, T.; Bose, A. Chandra, E-mail: acbose@nitt.edu

2016-05-23

Variation in photoluminescence (PL) properties of Eu{sup 3+} and Tb{sup 3+} as a function of co-dopant (Tb{sup 3+}) concentration are studied for Gd{sub 2-x-y}O{sub 3}: Eu{sup 3+}{sub x} Tb{sup 3+}{sub y} (x = 0.02, y = 0.01, 0.03, 0.05). The crystal structure analysis is carried out by X-ray Diffraction (XRD). Absence of addition peaks corresponding europium or terbium phase confirms the phase purity. Diffuse reflectance spectroscopy (DRS) reveals the absorption peaks corresponding to host matrix, Eu{sup 3+} and Tb{sup 3+}. The bandgap calculated from Kubelka – Munk function is also reported. PL spectra are recorded at the excitation wavelength ofmore » 307 nm and the emission peak corresponding to Eu{sup 3+} confirms the energy transfer from Tb{sup 3+} to Eu{sup 3+}. The agglomeration of particles acts as quenching centres for energy transfer at higher concentrations.« less

Exploring the role of genome and structural ions in preventing viral capsid collapse during dehydration

NASA Astrophysics Data System (ADS)

Martín-González, Natalia; Guérin Darvas, Sofía M.; Durana, Aritz; Marti, Gerardo A.; Guérin, Diego M. A.; de Pablo, Pedro J.

2018-03-01

Even though viruses evolve mainly in liquid milieu, their horizontal transmission routes often include episodes of dry environment. Along their life cycle, some insect viruses, such as viruses from the Dicistroviridae family, withstand dehydrated conditions with presently unknown consequences to their structural stability. Here, we use atomic force microscopy to monitor the structural changes of viral particles of Triatoma virus (TrV) after desiccation. Our results demonstrate that TrV capsids preserve their genome inside, conserving their height after exposure to dehydrating conditions, which is in stark contrast with other viruses that expel their genome when desiccated. Moreover, empty capsids (without genome) resulted in collapsed particles after desiccation. We also explored the role of structural ions in the dehydration process of the virions (capsid containing genome) by chelating the accessible cations from the external solvent milieu. We observed that ion suppression helps to keep the virus height upon desiccation. Our results show that under drying conditions, the genome of TrV prevents the capsid from collapsing during dehydration, while the structural ions are responsible for promoting solvent exchange through the virion wall.

PEPFAR support for the scaling up of collaborative TB/HIV activities.

PubMed

Howard, Andrea A; Gasana, Michel; Getahun, Haileyesus; Harries, Anthony; Lawn, Stephen D; Miller, Bess; Nelson, Lisa; Sitienei, Joseph; Coggin, William L

2012-08-15

The US President's Emergency Plan for AIDS Relief (PEPFAR) has supported a comprehensive package of care in which interventions to address HIV-related tuberculosis (TB) have received increased funding and support in recent years. PEPFAR's TB/HIV programming is based on the World Health Organization's 12-point policy for collaborative TB/HIV activities, which are integrated into PEPFAR annual guidance. PEPFAR implementing partners have provided crucial support to TB/HIV collaboration, and as a result, PEPFAR-supported countries in sub-Saharan Africa have made significant gains in HIV testing and counseling of TB patients and linkages to HIV care and treatment, intensified TB case finding, and TB infection control. PEPFAR's support of TB/HIV integration has also included significant investment in health systems, including improved laboratory services and educating and enlarging the workforce. The scale-up of antiretroviral therapy along with support of programs to increase HIV counseling and testing and improve linkage and retention in HIV care may have considerable impact on TB morbidity and mortality, if used synergistically with isoniazid preventive therapy, intensified case finding, and infection control. Issues to be addressed by future programming include accelerating implementation of isoniazid preventive therapy, increasing access and ensuring appropriate use of new TB diagnostics, supporting early initiation of antiretroviral therapy for HIV-infected TB patients, and strengthening systems to monitor and evaluate program implementation.

PEPFAR Support for the Scaling Up of Collaborative TB/HIV Activities

PubMed Central

Howard, Andrea A.; Gasana, Michel; Getahun, Haileyesus; Harries, Anthony; Lawn, Stephen D.; Miller, Bess; Nelson, Lisa; Sitienei, Joseph; Coggin, William L.

2014-01-01

The US President’s Emergency Plan for AIDS Relief (PEPFAR) has supported a comprehensive package of care in which interventions to address HIV-related tuberculosis (TB) have received increased funding and support in recent years. PEPFAR’s TB/HIV programming is based on the World Health Organization 12-point policy for collaborative TB/HIV activities, which are integrated into PEPFAR annual guidance. PEPFAR implementing partners have provided crucial support to TB/HIV collaboration, and as a result PEPFAR-supported countries in sub-Saharan Africa have made significant gains in HIV testing and counseling of TB patients and linkages to HIV care and treatment, intensified TB case finding, and TB infection control. PEPFAR’s support of TB/HIV integration has also included significant investment in health systems, including improved laboratory services and educating and enlarging the workforce. The scale-up of antiretroviral therapy along with support of programs to increase HIV counseling and testing and improve linkage and retention in HIV care may have considerable impact on TB morbidity and mortality, if used synergistically with isoniazid preventive therapy (IPT), intensified case finding and infection control. Issues to be addressed by future programming include accelerating implementation of IPT, increasing access and ensuring appropriate use of new TB diagnostics, supporting early initiation of antiretroviral therapy for HIV-infected TB patients, and strengthening systems to monitor and evaluate program implementation. PMID:22797735

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

SINEs, evolution and genome structure in the opossum.

PubMed

Gu, Wanjun; Ray, David A; Walker, Jerilyn A; Barnes, Erin W; Gentles, Andrew J; Samollow, Paul B; Jurka, Jerzy; Batzer, Mark A; Pollock, David D

2007-07-01

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.

Cost-Effectiveness of Initiating Antiretroviral Therapy at Different Points in TB Treatment in HIV-TB Coinfected Ambulatory Patients in South Africa.

PubMed

Naidoo, Kogieleum; Grobler, Anneke C; Deghaye, Nicola; Reddy, Tarylee; Gengiah, Santhanalakshmi; Gray, Andrew; Abdool Karim, Salim

2015-08-15

Initiation of antiretroviral therapy (ART) during tuberculosis (TB) treatment improves survival in TB-HIV coinfected patients. In patients with CD4 counts <50 cells per cubic millimeter, there is a substantial clinical and survival benefit of early ART initiation. The purpose of this study was to assess the costs and cost-effectiveness of starting ART at various time points during TB treatment in patients with CD4 counts ≥50 cells per cubic millimeter. In the SAPiT trial, 642 HIV-TB coinfected patients were randomized to 3 arms: receiving ART within 4 weeks of starting TB treatment (early treatment arm; Arm-1), after the intensive phase of TB treatment (late treatment arm; Arm-2), or after completing TB treatment (sequential arm; Arm-3). Direct health care costs were measured from a provider perspective using a micro-costing approach. The incremental cost per death averted was calculated using the trial outcomes. For patients with CD4 count ≥50 cells per cubic millimeter, median monthly variable costs per patient were US $116, US $113, and US $102 in Arm-1, Arm-2 and Arm-3, respectively. There were 12 deaths in 177 patients in Arm-1, 8 deaths in 180 patients in the Arm-2, and 19 deaths in 172 patients in Arm-3. Although the costs were lower in Arm-3, it had a substantially higher mortality rate. The incremental cost per death averted associated with moving from Arm-3 to Arm-2 was US $4199. There was no difference in mortality between Arm-1 and Arm-2, but Arm-1 was slightly more expensive. Initiation of ART after the completion of the intensive phase of TB treatment is cost-effective for patients with CD4 counts ≥50 cells per cubic millimeter.

Multiplex analysis of plasma cytokines/chemokines showing different immune responses in active TB patients, latent TB infection and healthy participants.

PubMed

Yao, Xiangyang; Liu, Yongliang; Liu, Yang; Liu, Wei; Ye, Zhizhong; Zheng, Chao; Ge, Shengxiang

2017-12-01

Interferon gamma release assays (IGRAs) have been widely used to diagnose Mycobacterium tuberculosis (MTB) infection. However, IGRAs cannot discriminate between active TB patients and latent TB infection (LTBI), and the sensitivity of IGRAs for MTB infection is suboptimal. Here, we analyzed cytokines/chemokines in MTB antigen-stimulated and -unstimulated plasma samples to identify host biomarkers that are associated with active TB and MTB infection. Active TB patients, subjects with LTBI and healthy participants were recruited. Seventy-one soluble cytokines and chemokines were tested using Luminex liquid array-based multiplexed immunoassays. For the 71 examined factors, our results indicated that the unstimulated levels of IL-8 Nil , IP-10 Nil , MIP-1a Nil , and sIL-2Ra Nil and the antigen stimulated levels of IL-8 (Ag-Nil) , VEGF (Ag-Nil) , and MCP-3 (Ag-Nil) were potential biomarkers for differentiating between active TB and LTBI, with AUCs of 0.8, 0.86, 0.755, 0.845, 0.825, 0.812 and 0.75, respectively. The G-CSF (Ag-Nil) , GM-CSF (Ag-Nil) , IL-1a (Ag-Nil) , IL-2 (Ag-Nil) , IP-10 (Ag-Nil) , BCA-1 (Ag-Nil) and Eotaxin-1 (Ag-Nil) responses were significantly higher in patients with active TB and LTBI compared with healthy participants (p < 0.05), with AUCs of 0.922, 0.902, 0.908, 1.0, 0.937, 0.919 and 0.935, respectively. Our preliminary data suggest that unstimulated or stimulated levels of cytokines and chemokines could be used as host biomarkers for diagnosing active TB as well as additional biomarkers, except IFN-γ, for MTB infection. Copyright © 2017 Elsevier Ltd. All rights reserved.

Opportunities and challenges for HIV care in overlapping HIV and TB epidemics.

PubMed

Havlir, Diane V; Getahun, Haileyesus; Sanne, Ian; Nunn, Paul

2008-07-23

Tuberculosis (TB) and the emerging multidrug-resistant TB epidemic represent major challenges to human immunodeficiency virus (HIV) care and treatment programs in resource-limited settings. Tuberculosis is a major cause of mortality among patients with HIV and poses a risk throughout the course of HIV disease, even after successful initiation of antiretroviral therapy (ART). Progress in the implementation of activities directed at reducing TB burden in the HIV population lags far behind global targets. HIV programs designed for longitudinal care are ideally suited to implement TB control measures and have no option but to address TB vigorously to save patient lives, to safeguard the massive investment in HIV treatment, and to curb the global TB burden. We propose a framework of strategic actions for HIV care programs to optimally integrate TB into their services. The core activities of this framework include intensified TB case finding, treatment of TB, isoniazid preventive treatment, infection control, administration of ART, TB recording and reporting, and joint efforts of HIV and TB programs at the national and local levels.

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

PubMed

Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

2014-11-29

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation

46 CFR 35.40-20 - Emergency equipment-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Emergency equipment-TB/ALL. 35.40-20 Section 35.40-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-20 Emergency equipment—TB/ALL. Each locker and space where emergency equipment is...

46 CFR 35.40-20 - Emergency equipment-TB/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Emergency equipment-TB/ALL. 35.40-20 Section 35.40-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-20 Emergency equipment—TB/ALL. Each locker and space where emergency equipment is...

46 CFR 35.40-20 - Emergency equipment-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Emergency equipment-TB/ALL. 35.40-20 Section 35.40-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-20 Emergency equipment—TB/ALL. Each locker and space where emergency equipment is...

46 CFR 35.40-20 - Emergency equipment-TB/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Emergency equipment-TB/ALL. 35.40-20 Section 35.40-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-20 Emergency equipment—TB/ALL. Each locker and space where emergency equipment is...

46 CFR 35.40-20 - Emergency equipment-TB/ALL.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Emergency equipment-TB/ALL. 35.40-20 Section 35.40-20 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-20 Emergency equipment—TB/ALL. Each locker and space where emergency equipment is...

46 CFR 35.40-6 - Emergency lights-TB/ALL.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Emergency lights-TB/ALL. 35.40-6 Section 35.40-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-6 Emergency lights—TB/ALL. Emergency lights must be marked in accordance with...

46 CFR 35.40-6 - Emergency lights-TB/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Emergency lights-TB/ALL. 35.40-6 Section 35.40-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-6 Emergency lights—TB/ALL. Emergency lights must be marked in accordance with...

46 CFR 35.40-6 - Emergency lights-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Emergency lights-TB/ALL. 35.40-6 Section 35.40-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-6 Emergency lights—TB/ALL. Emergency lights must be marked in accordance with...

46 CFR 35.40-6 - Emergency lights-TB/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Emergency lights-TB/ALL. 35.40-6 Section 35.40-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-6 Emergency lights—TB/ALL. Emergency lights must be marked in accordance with...

46 CFR 35.40-6 - Emergency lights-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Emergency lights-TB/ALL. 35.40-6 Section 35.40-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-6 Emergency lights—TB/ALL. Emergency lights must be marked in accordance with...

Adaptive potential of genomic structural variation in human and mammalian evolution.

PubMed

Radke, David W; Lee, Charles

2015-09-01

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

PubMed Central

Wilks, Christopher; Cline, Melissa S.; Weiler, Erich; Diehkans, Mark; Craft, Brian; Martin, Christy; Murphy, Daniel; Pierce, Howdy; Black, John; Nelson, Donavan; Litzinger, Brian; Hatton, Thomas; Maltbie, Lori; Ainsworth, Michael; Allen, Patrick; Rosewood, Linda; Mitchell, Elizabeth; Smith, Bradley; Warner, Jim; Groboske, John; Telc, Haifang; Wilson, Daniel; Sanford, Brian; Schmidt, Hannes; Haussler, David; Maltbie, Daniel

2014-01-01

The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. The CGHub currently contains >1.4 PB of data, has grown at an average rate of 50 TB a month and serves >100 TB per week. The architecture of CGHub is designed to support bulk searching and downloading through a Web-accessible application programming interface, enforce patient genome confidentiality in data storage and transmission and optimize for efficiency in access and transfer. In this article, we describe the design of these three components, present performance results for our transfer protocol, GeneTorrent, and finally report on the growth of the system in terms of data stored and transferred, including estimated limits on the current architecture. Our experienced-based estimates suggest that centralizing storage and computational resources is more efficient than wide distribution across many satellite labs. Database URL: https://cghub.ucsc.edu PMID:25267794

Persistence of collective behavior at high spin in the N = 88 nucleus Tb 153

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

Hartley, D. J.; Riley, M. A.; Wang, X.

Excited states in the N = 88 nucleus Tb-153 were observed up to spin similar to 40 in an experiment utilizing the Gammasphere array. The Tb-153 states were populated in a weak alpha 4n evaporation channel of the Cl-37 + Sn-124 reaction. Two previously known sequences were extended to higher spins, and a new decoupled structure was identified. The pi h(11/2) band was observed in the spin region where other N = 88 isotopes exhibit effects of prolate to oblate shape changes leading to band termination along the yrast line, whereas Tb-153 displays a persistent collective behavior. However, minor perturbationsmore » of the very highest state in both signatures of this h(11/2) band are observed, which perhaps signal the start of the transition towards band termination.« less

46 CFR 35.40-25 - Fire extinguishers-TB/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Fire extinguishers-TB/ALL. 35.40-25 Section 35.40-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-25 Fire extinguishers—TB/ALL. Each fire extinguisher shall be marked with a number...

46 CFR 35.40-25 - Fire extinguishers-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Fire extinguishers-TB/ALL. 35.40-25 Section 35.40-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-25 Fire extinguishers—TB/ALL. Each fire extinguisher shall be marked with a number...

46 CFR 35.40-35 - Rudder orders-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Rudder orders-TB/ALL. 35.40-35 Section 35.40-35 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-35 Rudder orders—TB/ALL. At all steering stations, there shall be installed a suitable...

46 CFR 35.40-35 - Rudder orders-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Rudder orders-TB/ALL. 35.40-35 Section 35.40-35 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-35 Rudder orders—TB/ALL. At all steering stations, there shall be installed a suitable...

46 CFR 35.40-35 - Rudder orders-TB/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Rudder orders-TB/ALL. 35.40-35 Section 35.40-35 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-35 Rudder orders—TB/ALL. At all steering stations, there shall be installed a suitable...

46 CFR 35.40-25 - Fire extinguishers-TB/ALL.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 1 2012-10-01 2012-10-01 false Fire extinguishers-TB/ALL. 35.40-25 Section 35.40-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-25 Fire extinguishers—TB/ALL. Each fire extinguisher shall be marked with a number...

46 CFR 35.40-35 - Rudder orders-TB/ALL.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Rudder orders-TB/ALL. 35.40-35 Section 35.40-35 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-35 Rudder orders—TB/ALL. At all steering stations, there shall be installed a suitable...

46 CFR 35.40-25 - Fire extinguishers-TB/ALL.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 1 2010-10-01 2010-10-01 false Fire extinguishers-TB/ALL. 35.40-25 Section 35.40-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-25 Fire extinguishers—TB/ALL. Each fire extinguisher shall be marked with a number...

46 CFR 35.40-25 - Fire extinguishers-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Fire extinguishers-TB/ALL. 35.40-25 Section 35.40-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL § 35.40-25 Fire extinguishers—TB/ALL. Each fire extinguisher shall be marked with a number...

46 CFR 35.40-35 - Rudder orders-TB/ALL.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 1 2011-10-01 2011-10-01 false Rudder orders-TB/ALL. 35.40-35 Section 35.40-35 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Posting and Marking Requirements-TB/ALL. § 35.40-35 Rudder orders—TB/ALL. At all steering stations, there shall be installed a suitable...

Prevalence and Risk factors for Drug Resistance among Hospitalized TB Patients in Georgia

PubMed Central

Vashakidze, L; Salakaia, A.; Shubladze, N.; Cynamon, M.; Barbakadze, K.; Kikvidze, M.; Papitashvili, L.; Nonikashvili, M.; Solomonia, N.; Bejanishvili, N.; Khurtsilava, I.

2010-01-01

SUMMARY Background Tuberculosis control in Georgia follows the WHO recommended DOTS strategy and has reached Global TB Control targets in treatment of sensitive TB, but the management of drug resistant forms of TB still represents a serious problem. A country-wide Drug Resistance Survey (DRS) found that the prevalence of MDR-TB was 6.8% in new and 27.4% in previously treated TB cases. Objective To determine prevalence and risk factors for drug resistance among TB patients in order to improve DR-TB case management and control. Methods Extensive social, clinical and bacteriological data were collected from hospitalized patients (National Centre for Tuberculosis and Lung Diseases, Georgia, 2005–2007). Results Out of 605 patients DR-TB was found in 491 (81.2%) cases, MDR-TB was observed in 261(43.1%) [51 (23%) out of 222 New cases and 210 (55%) out of 383 Previously treated cases], mono-DR-TB in 130 (21.5%), poly-DR-TB in 67 (11.1%) and XDR-TB in 33 (5.5%) cases. Study showed that female gender, living in densely populated capital, family TB contact and previous TB treatment are associated with risk for having MDR-TB. Conclusions Findings confirm the necessity of improvement of infection control measures and availability of standardized treatment for DR-TB patients. PMID:19723406

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts.

PubMed

Durand-Dubief, Mickaël; Absalon, Sabrina; Menzer, Linda; Ngwabyt, Sandra; Ersfeld, Klaus; Bastin, Philippe

2007-12-01

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

GDC 2: Compression of large collections of genomes

PubMed Central

Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

2015-01-01

The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about. PMID:26108279

GDC 2: Compression of large collections of genomes.

PubMed

Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

2015-06-25

The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.

Impact of ART on TB case fatality stratified by CD4 count for HIV-positive TB patients in Cape Town, South Africa (2009-2011).

PubMed

Kaplan, Richard; Caldwell, Judy; Middelkoop, Keren; Bekker, Linda-Gail; Wood, Robin

2014-08-15

To identify determinants of tuberculosis (TB) case fatality including the impact of antiretroviral therapy (ART) at different CD4 thresholds for HIV-positive adult and adolescent TB patients. Through a retrospective analysis of the electronic TB database, we identified the HIV status of newly registered patients aged ≥15 years. Multivariable Cox proportional hazard models were used to determine the risk factors for TB case fatality in these patients. In 2009, 2010, and 2011, 25,841, 26,104, and 25,554 newly registered adult TB patients were treated in primary health care clinics in Cape Town, of whom 49.7%, 50.4%, and 50.9% were HIV positive. ART uptake increased over 3 years from 43% to 64.9%, and case fatality of the HIV-positive patients decreased from 7.0% to 5.8% (P < 0.001). Female gender, increasing age, retreatment TB, low CD4 counts, and extrapulmonary TB were associated with increased case fatality, whereas patients on ART had a substantial decrease in case fatality. The difference in case fatality between patients on ART and not on ART was most pronounced at low CD4 counts with the positive influence of ART noted up to a CD4 count threshold of 350 cells per cubic millimeter (P < 0.001). Despite improvements in ART uptake, in 2011, 21% of the patients with CD4 counts <350 cells per cubic millimeter did not start ART during TB treatment. This study showed a relatively poor uptake of ART among severely immune-compromised TB patients. Patients with CD4 counts <350 cells per cubic millimeter were shown to clearly benefit from ART during TB treatment, and ART initiation should be prioritized for this category of patients.

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence.

PubMed

de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Tobes, Raquel; Manrique, Marina; López, Vladimir; Romero, Beatriz; Bezos, Javier; Dominguez, Lucas; Sevilla, Iker A; Garrido, Joseba M; Juste, Ramón; Madico, Guillermo; Jones-López, Edward; Gortazar, Christian

2015-11-01

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

PubMed Central

de la Fuente, José; Díez-Delgado, Iratxe; Contreras, Marinela; Vicente, Joaquín; Cabezas-Cruz, Alejandro; Tobes, Raquel; Manrique, Marina; López, Vladimir; Romero, Beatriz; Bezos, Javier; Dominguez, Lucas; Sevilla, Iker A.; Garrido, Joseba M.; Juste, Ramón; Madico, Guillermo; Jones-López, Edward; Gortazar, Christian

2015-01-01

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to

TB Mobile: a mobile app for anti-tuberculosis molecules with known targets

PubMed Central

2013-01-01

Background An increasing number of researchers are focused on strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs. Results In order to learn from prior work we have collated information on molecules screened versus Mtb and their targets which has been made available in the Collaborative Drug Discovery (CDD) database. This dataset contains published data on target, essentiality, links to PubMed, TBDB, TBCyc (which provides a pathway-based visualization of the entire cellular biochemical network) and human homolog information. The development of mobile cheminformatics apps could lower the barrier to drug discovery and promote collaboration. Therefore we have used this set of over 700 molecules screened versus Mtb and their targets to create a free mobile app (TB Mobile) that displays molecule structures and links to the bioinformatics data. By input of a molecular structures and performing a similarity search within the app we can infer potential targets or search by targets to retrieve compounds known to be active. Conclusions TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The app is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts. PMID:23497706

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

PubMed Central

Theis, Corinna; Zirbel, Craig L.; zu Siederdissen, Christian Höner; Anthon, Christian; Hofacker, Ivo L.; Nielsen, Henrik; Gorodkin, Jan

2015-01-01

Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence. PMID:26509713

Electrocatalysis of carbon black- or poly(diallyldimethylammonium chloride)-functionalized activated carbon nanotubes-supported Pd-Tb towards methanol oxidation in alkaline media

NASA Astrophysics Data System (ADS)

Wang, Li; Wang, Yi; Li, An; Yang, Yunshang; Tang, Qinghu; Cao, Hongbin; Qi, Tao; Li, Changming

2014-07-01

The Pd-Tb/C catalysts with different Pd/Tb ratios were synthesized by a simple simultaneous reduction reaction with sodium borohydride in aqueous solution. The structure and morphology of those catalysts had been characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The electrocatalytic performance of those catalysts for methanol oxidation in alkaline media was investigated using cyclic voltammetry (CV), linear sweep voltammetry (LSV) and CO stripping experiments. It is found that the 20%Pd-1%Tb/C catalyst has a higher catalytic activity than the 20%Pd/C catalyst, but the effect of Tb cannot be explained by a bi-functional mechanism. According to the X-Ray photoelectron spectroscopy (XPS) analyses, it is suggested that the higher content of metallic Pd caused by the addition of Tb contributes to the better catalytic activity of 20%Pd-1%Tb/C. Based on the good electrocatalytic performance of 20%Pd-1%Tb/C, the 20%Pd-1%Tb catalyst supported on poly(diallyldimethylammonium chloride) (PDDA)-functionalized activated carbon nanotubes was prepared, and it exhibits a better catalytic activity. The improvement mainly results from the further increase of metallic Pd due to the presence of PDDA.

Growth and magnetooptical properties of anisotropic TbF3 single crystals

NASA Astrophysics Data System (ADS)

Valiev, Uygun V.; Karimov, Denis N.; Burdick, Gary W.; Rakhimov, Rakhim; Pelenovich, Vasiliy O.; Fu, Dejun

2017-06-01

This paper investigates the Faraday effect and absorption and luminescence spectra of single-crystal TbF3 measured at 90 K and 300 K. The optical-quality single-phase TbF3 crystals (structural type β-YF3) were grown by the Bridgman technique. Faraday rotation angles were measured at remagnetization along the [100] crystallographic axis. Low temperature optical measurements were carried out along the [100] axis. "Quasi-doublet" sublevels with energy at 0 cm-1, 65 cm-1, and 190 cm-1, and also a singlet sublevel with energy at 114 cm-1 located in the ground 7F6 multiplet were determined from the low temperature luminescence spectra. The Van-Vleck behavior of the magnetic susceptibility χb can be satisfactorily explained by the magnetic mixing of wave functions belonging to the ground and first excited "quasi-doublet" sublevels at 0 and 65 cm-1, respectively. Analysis of the oscillation dependences of the rotation angle showed that the value of the natural birefringence (Δn ≈ 0.0186) remains nearly constant within the wavelength and temperature ranges under investigation. As the temperature decreases, we find significant increases in the oscillation amplitude of the rotation angle and in the Verdet constant V. The spectral dependences V(χ) are linear throughout the temperature range. The magnetooptical activity of TbF3 can be explained by means of the spin- and parity-allowed electric-dipole 4f → 5d transitions in the Tb3+ ions.

G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures.

PubMed

Solomon, Oz; Kunik, Vered; Simon, Amos; Kol, Nitzan; Barel, Ortal; Lev, Atar; Amariglio, Ninette; Somech, Raz; Rechavi, Gidi; Eyal, Eran

2016-08-26

Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D . G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery

PubMed Central

Swain, Martin T.; Larkin, Denis M.; Caffrey, Conor R.; Davies, Stephen J.; Loukas, Alex; Skelly, Patrick J.; Hoffmann, Karl F.

2011-01-01

Schistosoma genomes provide a comprehensive resource for identifying the molecular processes that shape parasite evolution and for discovering novel chemotherapeutic or immunoprophylactic targets. Here, we demonstrate how intra- and intergenus comparative genomics can be used to drive these investigations forward, illustrate the advantages and limitations of these approaches and review how post genomic technologies offer complementary strategies for genome characterisation. While sequencing and functional characterisation of other schistosome/platyhelminth genomes continues to expedite anthelmintic discovery, we contend that future priorities should equally focus on improving assembly quality, and chromosomal assignment, of existing schistosome/platyhelminth genomes. PMID:22024648

Mixing Enthalpies of TbBr3-MBr Liquid Mixtures

NASA Astrophysics Data System (ADS)

Rycerz, L.; Gaune-Escard, M.

2001-12-01

The molar enthalpies of mixing, Δmix Hm in the binary liquid systems TbBr3-MBr (M = Li, Na, K, Rb, Cs) have been m easured with a Calvet-type high-tem perature microcalorimeter over the entire composition range with an accuracy of about 6 %. Mixing of the two liquid components was achieved by using the "break-off am poule" technique. All the investigated systems show negative enthalpies of mixing with a minim um value of approxim ately -1.25, - 8 .3 , -17.0, - 2 0 . 0 and -22.5 kJ mol -1, for M = Li, Na, K, Rb and Cs, respectively. The mixing enthalpy in the TbBr3- LiBr system is positive in the TbBr3-rich region. For all the systems, the enthalpy minimum occurs at mole fraction xTbBr3 ≈ 0.3 - 0.4. The molar enthalpies of form ation Δ formHm (3MBr, TbBr3, 1) for M = Li, Na, K, Rb and Cs at 1113 K (arising from the reaction 3M Br(1) +TbBr3(1) = (3MBr, TbBr3) (1)) are found to be -4 .8 , -31.3, -63.3, -70.3 and -8 1 .2 kJ mol-1 , respectively. The leastsquares coefficients A, B, C, D and E in the equation λ (kJ mol-1) = A + B x + C x2 + Dx3 + Ex4, where A is an interaction param eter and x = xTbBr , are also reported.

Mycobacteriophages: an important tool for the diagnosis of Mycobacterium tuberculosis (review).

PubMed

Fu, Xiaoyan; Ding, Mingxing; Zhang, Ning; Li, Jicheng

2015-07-01

The prevention and control of tuberculosis (TB) on a global scale has become increasingly important with the emergence of multidrug‑resistant TB. Mycobacterium tuberculosis phages have been identified as an important investigative tool. Phage genomes exhibit a significant level of diversity and mosaic genome architecture, however, they are simple structures, which are amenable to genetic manipulation. Based on these characteristics, the phages may be used to construct a shuttle plasmid, which is an indispensable tool in the investigation of TB. Furthermore, they may be used for rapid diagnosis and assessing drug susceptibility of TB, including phage amplified assessment and reporter phage technology. With an improved understanding of mycobacteriophages, further clarification of the pathogenesis of TB, and of the implications for its diagnosis and therapy, may be elucidated.

The effect of HIV coinfection, HAART and TB treatment on cytokine/chemokine responses to Mycobacterium tuberculosis (Mtb) antigens in active TB patients and latently Mtb infected individuals.

PubMed

Kassa, Desta; de Jager, Wilco; Gebremichael, Gebremedhin; Alemayehu, Yodit; Ran, Leonie; Fransen, Justin; Wolday, Dawit; Messele, Tsehaynesh; Tegbaru, Belete; Ottenhoff, Tom H M; van Baarle, Debbie

2016-01-01

Identification of Mtb specific induced cytokine/chemokine host biomarkers could assist in developing novel diagnostic, prognostic and therapeutic tools for TB. Levels of IFN-γ, IL-2, IL-17, IL-10, IP-10 and MIP-1α were measured in supernatants of whole blood stimulated with Mtb specific fusion protein ESAT-6/CFP-10 using xMAP technology. The study groups were HIV positive TB patients (HIV(+)TB(+)), HIV negative TB patients (HIV(-)TB(+)), HIV positive tuberculin skin test positive (TST+) (HIV(+)TST(+)), HIV negative TST+ (HIV(-)TST(+)), and HIV(-)TST(-) individuals. Compared to HIV(-)TST(-), latent TB infection led to increased levels of IP-10, IFN-γ and IL-17, while levels of IL-2 and IP-10 were increased with active TB. Levels of IFN-γ, IL-17, MIP-1α, and IL-10 were increased in HIV(-)TST(+) individuals compared to HIV(-)TB(+) patients. HIV coinfection decreased the level of IFN-γ, IL-17, IP-10 and IL-2. After six months (M6) of anti-TB treatment (ATT) in HIV(-)TB(+) patients, IFN-γ, IL-10, and MIP-1α levels normalized. After M6 and M18 of ATT plus HAART in HIV(+)TB(+) patients, levels of MIP-1α and IL-10 normalized, while this was not the case for IFN-γ, IL-2, IL-17, and IP-10 levels. In HIV(+)TST(+) patients on HAART, levels of IFN-γ, IL-17, IL-10 and MIP-1α normalized, while no change in the levels of IL-2 and IP-10 were observed. In conclusion, the simultaneous measurement of IFN-γ, IL-17 and IP-10 may assist in diagnosing LTBI; IL-2 and IP-10 may assist in diagnosing active TB; while IFN-γ, IL-17, MIP-1α, and IL-10 levels could help to discriminate LTBI and active TB. In addition, IL-10 and MIP-1α levels could help to monitor responses to TB treatment and HAART. Copyright © 2015 Elsevier Ltd. All rights reserved.

Formation of Ag nanoparticles and enhancement of Tb3+ luminescence in Tb and Ag co-doped lithium-lanthanum-aluminosilicate glass

NASA Astrophysics Data System (ADS)

Piasecki, Patryk; Piasecki, Ashley; Pan, Zhengda; Mu, Richard; Morgan, Steven H.

2010-12-01

Tb3+ and Ag co-doped glass nano-composites were synthesized in a glass matrix Li2O-LaF3-Al2O3-SiO2 (LLAS) by a melt-quench technique. The growth of Ag nanoparticles (NPs) was controlled by a thermal annealing process. A broad absorption band peaking at about 420 nm was observed due to surface plasmon resonance (SPR) of Ag NPs. The intensity of this band grows with increasing annealing time. The transmission electron microscopic image (TEM) reveals the formation of Ag NPs in glass matrix. Photoluminescence (PL) emission and excitation spectra were measured for glass samples with different Ag concentrations and different annealing times. Plasmon enhanced Tb3+ luminescence was observed at certain excitation wavelength regions. Luminescence quenching was also observed for samples with high Ag concentration and longer annealing time. Our luminescence results suggest that there are two competitive effects, enhancement and quenching, acting on Tb3+ luminescence in the presence of Ag NPs. The enhancement of Tb3+ luminescence is mainly attributed to local field effects due to SPR. The quenching of luminescence suggests an energy transfer from Tb3+ ions to Ag NPs.

Estimating the effect of lay knowledge and prior contact with pulmonary TB patients, on health-belief model in a high-risk pulmonary TB transmission population.

PubMed

Zein, Rizqy Amelia; Suhariadi, Fendy; Hendriani, Wiwin

2017-01-01

The research aimed to investigate the effect of lay knowledge of pulmonary tuberculosis (TB) and prior contact with pulmonary TB patients on a health-belief model (HBM) as well as to identify the social determinants that affect lay knowledge. Survey research design was conducted, where participants were required to fill in a questionnaire, which measured HBM and lay knowledge of pulmonary TB. Research participants were 500 residents of Semampir, Asemrowo, Bubutan, Pabean Cantian, and Simokerto districts, where the risk of pulmonary TB transmission is higher than other districts in Surabaya. Being a female, older in age, and having prior contact with pulmonary TB patients significantly increase the likelihood of having a higher level of lay knowledge. Lay knowledge is a substantial determinant to estimate belief in the effectiveness of health behavior and personal health threat. Prior contact with pulmonary TB patients is able to explain the belief in the effectiveness of a health behavior, yet fails to estimate participants' belief in the personal health threat. Health authorities should prioritize males and young people as their main target groups in a pulmonary TB awareness campaign. The campaign should be able to reconstruct people's misconception about pulmonary TB, thereby bringing around the health-risk perception so that it is not solely focused on improving lay knowledge.

Integrated Source Case Investigation for Tuberculosis (TB) and HIV in the Caregivers and Household Contacts of Hospitalised Young Children Diagnosed with TB in South Africa: An Observational Study

PubMed Central

Lala, Sanjay G.; Little, Kristen M.; Tshabangu, Nkeko; Moore, David P.; Msandiwa, Reginah; van der Watt, Martin; Chaisson, Richard E.; Martinson, Neil A.

2015-01-01

Background Contact tracing, to identify source cases with untreated tuberculosis (TB), is rarely performed in high disease burden settings when the index case is a young child with TB. As TB is strongly associated with HIV infection in these settings, we used source case investigation to determine the prevalence of undiagnosed TB and HIV in the caregivers and household contacts of hospitalised young children diagnosed with TB in South Africa. Methods Caregivers and household contacts of 576 young children (age ≤7 years) with TB diagnosed between May 2010 and August 2012 were screened for TB and HIV. The primary outcome was the detection of laboratory-confirmed, newly-diagnosed TB disease and/or HIV-infection in close contacts. Results Of 576 caregivers, 301 (52·3%) self-reported HIV-positivity. Newly-diagnosed HIV infection was detected in 63 (22·9%) of the remaining 275 caregivers who self-reported an unknown or negative HIV status. Screening identified 133 (23·1%) caregivers eligible for immediate anti-retroviral therapy (ART). Newly-diagnosed TB disease was detected in 23 (4·0%) caregivers. In non-caregiver household contacts (n = 1341), the prevalence of newly-diagnosed HIV infection and TB disease was 10·0% and 3·2% respectively. On average, screening contacts of every nine children with TB resulted in the identification of one case of newly-diagnosed TB disease, three cases of newly diagnosed HIV-infection, and three HIV-infected persons eligible for ART. Conclusion In high burden countries, source case investigation yields high rates of previously undiagnosed HIV and TB infection in the close contacts of hospitalised young children diagnosed with TB. Furthermore, integrated screening identifies many individuals who are eligible for immediate ART. Similar studies, with costing analyses, should be undertaken in other high burden settings–integrated source case investigation for TB and HIV should be routinely undertaken if our findings are confirmed

Constitution diagram on the system TlSe-Tb-Se

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

Guseinov, G.D.; Kerimova, E.M.; Agamaliev, D.G.

1988-03-01

The constitution diagram of the system TlSe-TbSe was constructed based on the results of differential-thermal, x-ray phase, and microstructural analyses and measurements of the microhardness. The compound TlTbSe/sub 2/, forming by a peritectic reaction, was observed. It was established that the solubility of TbSe in TlSe at room temperature equals 4.0 mole %.

Cost-effectiveness of initiating antiretroviral therapy at different points in TB treatment in HIV-TB co-infected ambulatory patients in South Africa

PubMed Central

Naidoo, Kogieleum; Grobler, Anneke C; Deghaye, Nicola; Reddy, Tarylee; Gengiah, Santhanalakshmi; Gray, Andrew; Karim, Salim Abdool

2015-01-01

Objective Initiation of antiretroviral therapy (ART) during tuberculosis (TB) treatment improves survival in TB-HIV co-infected patients. In patients with CD4+ counts <50cells/mm3, there is a substantial clinical and survival benefit of early ART initiation. The purpose of this study was to assess the costs and cost effectiveness of starting ART at various time points during TB treatment in patients with CD4+ counts ≥50cells/mm3. Methods In the SAPiT trial, 642 HIV-TB co-infected patients were randomized to three arms, either receiving ART within 4 weeks of starting TB treatment (early treatment arm; Arm-1), after the intensive phase of TB treatment (late treatment arm; Arm-2), or after completing TB treatment (sequential arm; Arm-3). Direct healthcare costs were measured from a provider perspective using a micro-costing approach. The incremental cost per death averted was calculated using the trial outcomes. Results For patients with CD4+ count≥50cells/mm3, median monthly variable costs per patient were $116, $113 and $102 in Arms-1, -2 and -3, respectively. There were 12 deaths in 177 patients in Arm-1, 8 deaths in 180 patients in the Arm-2 and 19 deaths in 172 patients in Arm-3. While the costs were lower in Arm-3, it had a substantially higher mortality rate. The incremental cost per death averted associated with moving from Arm-3 to Arm-2 was $4199. There was no difference in mortality between Arm-1 and Arm-2, but Arm-1 was slightly more expensive. Conclusions Initiation of ART after the completion of the intensive phase of TB treatment is cost effective for patients with CD4+ counts≥50cells/mm3. PMID:26167618

Structural and magnetic properties of two branches of the tripod-kagome-lattice family A2R3Sb3O14 (A = Mg, Zn; R = Pr, Nd, Gd, Tb, Dy, Ho, Er, Yb)

NASA Astrophysics Data System (ADS)

Dun, Z. L.; Trinh, J.; Lee, M.; Choi, E. S.; Li, K.; Hu, Y. F.; Wang, Y. X.; Blanc, N.; Ramirez, A. P.; Zhou, H. D.

2017-03-01

We present a systematic study of the structural and magnetic properties of two branches of the rare-earth tripod-kagome-lattice (TKL) family A2R3Sb3O14 (A = Mg, Zn; R = Pr, Nd, Gd, Tb, Dy, Ho, Er, Yb; here, we use abbreviation A-R, as in MgPr for Mg2Pr3Sb3O14 ), which complements our previously reported work on MgDy, MgGd, and MgEr [Z. L. Dun et al., Phys. Rev. Lett. 116, 157201 (2016), 10.1103/PhysRevLett.116.157201]. The present susceptibility (χdc, χac) and specific-heat measurements reveal various magnetic ground states, including the nonmagnetic singlet state for MgPr, ZnPr; long-range orderings (LROs) for MgGd, ZnGd, MgNd, ZnNd, and MgYb; a long-range magnetic charge ordered state for MgDy, ZnDy, and potentially for MgHo; possible spin-glass states for ZnEr, ZnHo; the absence of spin ordering down to 80 mK for MgEr, MgTb, ZnTb, and ZnYb compounds. The ground states observed here bear both similarities as well as striking differences from the states found in the parent pyrochlore systems. In particular, while the TKLs display a greater tendency towards LRO, the lack of LRO in MgHo, MgTb, and ZnTb can be viewed from the standpoint of a balance among spin-spin interactions, anisotropies, and non-Kramers nature of single-ion state. While substituting Zn for Mg changes the chemical pressure, and subtly modifies the interaction energies for compounds with larger R ions, this substitution introduces structural disorder and modifies the ground states for compounds with smaller R ions (Ho, Er, Yb).

Lithium-aluminum-zinc phosphate glasses activated with Tb3+ and Tb3+/Eu3+ for green laser medium, reddish-orange and white phosphor applications

NASA Astrophysics Data System (ADS)

Francisco-Rodriguez, H. I.; Lira, A.; Soriano-Romero, O.; Meza-Rocha, A. N.; Bordignon, S.; Speghini, A.; Lozada-Morales, R.; Caldiño, U.

2018-05-01

A spectroscopic analysis of Tb3+ and Tb3+/Eu3+ doped lithium-aluminum-zinc phosphate glasses is performed through their absorbance and photoluminescence spectra, and decay time profiles. Laser parameter values (stimulated emission cross section, effective bandwidth, gain bandwidth and optical gain) were obtained for the terbium 5D4 → 7F5 green emission from the Tb3+ singly-doped glass (LAZT) excited at 350 nm to judge the suitability of the glass phosphor for fiber lasers. A quantum yield of (47.68 ± 0.49)% was measured for the 5D4 level luminescence. Upon 350 nm excitation the LAZT glass phosphor emits green light with a color purity of 65.6% and chromaticity coordinates (0.285, 0.585) very close to those (0.29, 0.60) of European Broadcasting Union illuminant green. The Tb3+/Eu3+codoped glass emission color can be tuned from reddish-orange of 1865 K upon 318 nm excitation to warm white of 3599 K and neutral white of 4049 K upon 359 and 340 nm excitations, respectively. Upon Tb3+ excitation at 340 nm Eu3+ is sensitized by Tb3+ through a non-radiative energy transfer with an efficiency of 0.23-0.26. An electric dipole-dipole interaction might be the dominant mechanism in the Tb3+ to Eu3+ energy transfer taking place into Tb3+ - Eu3+ clusters.

Synthesis and anisotropic properties of single crystalline Ln{sub 2}Ru{sub 3}Al{sub 15+x} (Ln=Gd, Tb)

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

Morrison, Gregory; Prestigiacomo, Joseph; Haldolaarachchige, Neel

2016-04-15

Single crystals of Ln{sub 2}Ru{sub 3}Al{sub 15+x} (Ln=Gd, Tb) have been grown using the self-flux method under Ru-poor conditions. The structure of the Gd analog is found to be highly dependent on the synthesis method. Gd{sub 2}Ru{sub 3}Al{sub 15.08} orders antiferromagnetically at 17.5 K. Tb{sub 2}Ru{sub 3}Al{sub 15.05} enters an antiferromagnetic state at 16.6 K followed by a likely incommensurate-to-commensurate transition at 14.9 K for crystals oriented with H//ab. For crystals oriented with H//c, a broad maximum is observed in the temperature dependent M/H, indicative of a highly anisotropic magnetic system with the hard axis in the c-direction. The magnetizationmore » as a function of field and magnetoresistance along the ab-direction of Tb{sub 2}Ru{sub 3}Al{sub 15.05} display a stepwise behavior and indicate strong crystalline electric field effects. - Graphical abstract: Single crystal, structure, and highly anisotropic magnetoresistance due to strong crystalline electric field effects of Tb{sub 2}Ru{sub 3}Al{sub 15.05}. - Highlights: • Single crystals of Ln{sub 2}Ru{sub 3}Al{sub 15+x} were grown for the first time via flux growth. • The structure of Gd{sub 2}Ru{sub 3}Al{sub 15.09} differs from that of arc melted Gd{sub 2}Ru{sub 3.08}Al{sub 15}. • Tb{sub 2}Ru{sub 3}Al{sub 15.05} exhibits highly anisotropic magnetic and transport properties. • The properties of Tb{sub 2}Ru{sub 3}Al{sub 15.05} arise due to crystalline electric field effects.« less

Hierarchy Low CD4+/CD8+ T-Cell Counts and IFN-γ Responses in HIV-1+ Individuals Correlate with Active TB and/or M.tb Co-Infection.

PubMed

Shao, Lingyun; Zhang, Xinyun; Gao, Yan; Xu, Yunya; Zhang, Shu; Yu, Shenglei; Weng, Xinhua; Shen, Hongbo; Chen, Zheng W; Jiang, Weimin; Zhang, Wenhong

2016-01-01

Detailed studies of correlation between HIV-M.tb co-infection and hierarchy declines of CD8+/CD4+ T-cell counts and IFN-γ responses have not been done. We conducted case-control studies to address this issue. 164 HIV-1-infected individuals comprised of HIV-1+ATB, HIV-1+LTB and HIV-1+TB- groups were evaluated. Immune phenotyping and complete blood count (CBC) were employed to measure CD4+ and CD8+ T-cell counts; T.SPOT.TB and intracellular cytokine staining (ICS) were utilized to detect ESAT6, CFP10 or PPD-specific IFN-γ responses. There were significant differences in median CD4+ T-cell counts between HIV-1+ATB (164/μL), HIV-1+LTB (447/μL) and HIV-1+TB- (329/μL) groups. Hierarchy low CD4+ T-cell counts (<200/μL, 200-500/μL, >500/μL) were correlated significantly with active TB but not M.tb co-infection. Interestingly, hierarchy low CD8+ T-cell counts were not only associated significantly with active TB but also with M.tb co-infection (P<0.001). Immunologically, HIV-1+ATB group showed significantly lower numbers of ESAT-6-/CFP-10-specific IFN-γ+ T cells than HIV-1+LTB group. Consistently, PPD-specific IFN-γ+CD4+/CD8+ T effector cells in HIV-1+ATB group were significantly lower than those in HIV-1+LTB group (P<0.001). Hierarchy low CD8+ T-cell counts and effector function in HIV-1-infected individuals are correlated with both M.tb co-infection and active TB. Hierarchy low CD4+ T-cell counts and Th1 effector function in HIV-1+ individuals are associated with increased frequencies of active TB, but not M.tb co-infection.

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

PubMed

Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S

2005-12-08

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome

PubMed Central

Huang, Cheng Ran Lisa; Schneider, Anna M.; Lu, Yunqi; Niranjan, Tejasvi; Shen, Peilin; Robinson, Matoya A.; Steranka, Jared P.; Valle, David; Civin, Curt I.; Wang, Tao; Wheelan, Sarah J.; Ji, Hongkai; Boeke, Jef D.; Burns, Kathleen H.

2010-01-01

Summary Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further. PMID:20602999

Relationships between Gene Structure and Genome Instability in Flowering Plants.

PubMed

Bennetzen, Jeffrey L; Wang, Xuewen

2018-03-05

Flowering plant (angiosperm) genomes are exceptional in their variability with respect to genome size, ploidy, chromosome number, gene content, and gene arrangement. Gene movement, although observed in some of the earliest plant genome comparisons, has been relatively underinvestigated. We present herein a description of several interesting properties of plant gene and genome structure that are pertinent to the successful movement of a gene to a new location. These considerations lead us to propose a model that can explain the frequent success of plant gene mobility, namely that Small Insulated Genes Move Around (SIGMAR). The SIGMAR model is then compared with known processes for gene mobilization, and predictions of the SIGMAR model are formulated to encourage future experimentation. The overall results indicate that the frequent gene movement in angiosperm genomes is partly an outcome of the unusual properties of angiosperm genes, especially their small size and insulation from epigenetic silencing. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

46 CFR 39.1003 - Definitions-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Definitions-TB/ALL. 39.1003 Section 39.1003 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS VAPOR CONTROL SYSTEMS General § 39.1003 Definitions—TB/ALL. As used in this part only: Barge vapor connection means the point in a barge's piping...

46 CFR 39.1001 - Applicability-TB/ALL.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 1 2014-10-01 2014-10-01 false Applicability-TB/ALL. 39.1001 Section 39.1001 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS VAPOR CONTROL SYSTEMS General § 39.1001 Applicability—TB/ALL. (a) This part applies to tank vessels that use a vapor control system (VCS) to collect...

46 CFR 39.1001 - Applicability-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Applicability-TB/ALL. 39.1001 Section 39.1001 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS VAPOR CONTROL SYSTEMS General § 39.1001 Applicability—TB/ALL. (a) This part applies to tank vessels that use a vapor control system (VCS) to collect...

46 CFR 39.1003 - Definitions-TB/ALL.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 1 2013-10-01 2013-10-01 false Definitions-TB/ALL. 39.1003 Section 39.1003 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS VAPOR CONTROL SYSTEMS General § 39.1003 Definitions—TB/ALL. As used in this part only: Barge vapor connection means the point in a barge's piping...

Strengthening TB infection control in specialized health facilities in Romania--using a participatory approach.

PubMed

Turusbekova, N; Popa, C; Dragos, M; van der Werf, M J; Dinca, I

2016-02-01

In 2012, the tuberculosis (TB) notification rate among Romanian TB facility doctors and nurses was 7.2 times higher than in the general population. This indicates that transmission is ongoing inside TB facilities and that TB infection control measures are insufficient. To help prevent nosocomial TB transmission a project was implemented that aimed at providing nationwide tailor-made technical assistance in TB infection control (TB-IC) in TB treatment facilities, including the development of TB infection control plans. The objective of the present article is to describe the implementation of the project and to discuss successes and challenges. The project was an implementation study using two methods of evaluation: (1) a cross sectional questionnaire study; and (2) collection of information, during the training, on challenges related to infection control and to the project implementation. The project team developed a TB facility infection control (TB-IC) plan template, together with the Romanian experts. The template was discussed and agreed upon with the experts at a meeting and thereafter distributed by email to all TB facilities. Afterwards, a training of trainers (TOT) seminar was organized which included the provision of information about different training methods, as well as information about TB-IC. The TOT was followed by training for key TB-IC providers. Information about use of the TB-IC template was gathered through a self-administered questionnaire sent to all participants of the expert meeting and the training (42 people). Additionally, non-systematized discussions were held on broader challenges in TB-IC implementation during the training. Within the project 42 key TB-IC service providers were trained in TB-IC, including 9 who were trained at a TOT seminar. The trainees were specialists working at the national level, such as country TB coordinators, or at the TB facility level: TB doctors, epidemiologists, laboratory specialists and maintenance

Pattern of socio-economic and health aspects among TB patients and controls.

PubMed

Kapoor, A K; Deepani, Vijit; Dhall, Meenal; Kapoor, Satwanti

2016-10-01

Socio-economic and health-related factors have a significant impact on tuberculosis (TB) incidence among population residing in resource-scare settings. To evaluate the pattern of socio-economic and health-related factors among TB patients and control in Delhi, India. The present cross-sectional study was performed among 893 TB patients (or cases) and 333 healthy disease-free controls. The data for the present study was obtained from several district TB centres in north, west and south Delhi. The collected data was edited, coded and statistical analysed with the help of SPSS 20.0 version. Illiteracy and primary education were significant risk factors being associated with a TB. Rented housing condition had an odds ratio (OR) of 1.4 (95% confidence interval [CI]: 1.09-1.89) compared to owned housing condition. 3-5 individuals per room were 3 times more likely to be associated with a case of TB (95% CI: 2.49-4.41). Migrant individuals were 13 times more likely to be associated with a case of TB (95% CI: 8.77-19.78) in comparison to settled population. Daily consumption of non-vegetarian food also significantly contributed to case of TB with an OR of 3.4 (95% CI: 2.51-4.72). Loss of appetite and family TB served as significant health-related factors associated with TB risk. Lower educational status, rented household, individuals per room (as a measure of overcrowding) and migratory status served as prominent risk factors for TB disease. Preference and frequency of non-vegetarian food being consumed, night sweating, weight loss, loss of appetite, earlier TB and family TB were principle health-related risk factors associated with TB disease. Copyright © 2016 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.

HIV screening among TB patients and level of antiretroviral therapy and co-trimoxazole preventive therapy for TB/HIV patients in Hawassa University Referral Hospital: a five year retrospective study.

PubMed

Simieneh, Asnake; Hailemariam, Mengistu; Amsalu, Anteneh

2017-01-01

Initiation of antiretroviral therapy (ART) and co-trimoxazole preventive therapy (CPT) is recommended for tuberculosis (TB)/human immunodeficiency virus (HIV) co-infected patients to prevent opportunistic infection. The aim of this study was to assess the prevalence of HIV among TB patients and initiation of ART and provision of CPT for TB/HIV co-infected patients in Hawassa university referral hospital. A five year document review was done on 1961 TB patients who are registered at TB clinic of Hawassa university referral hospital from September 2009 to august 2014. Data were collected using checklist. Data analysis was done by using SPSS version 20 software. Bivariate and multivariate logistic regression analysis was used to determine the predictors of TB/HIV co-infection. Among 1961 TB patients diagnosed in the hospital, 95% (1765) were screened for HIV. Of these, 13.9% (246) were HIV positive. Out of 246 TB/HIV co-infected patients 31.7% (78/246) and 37.4% (92/246) were enrolled to start ART and CPT respectively. Roughly the trends of TB/HIV co-infection decreased with increased linkage to CPT, while linkage to ART was not regular across the year. The rate of TB/HIV co-infection was significantly associated with type of TB. Although, trend of HIV among TB patients has decreased across the year, only a minority of co-infected patients was linked to start ART and CPT. Therefore, screening of all TB patients for HIV and linkage of co-infected patients to HIV care to start ART and CPT should be strengthened in-line with the national guidelines.

Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies

PubMed Central

Sserwadda, Ivan; Amujal, Marion; Namatovu, Norah

2018-01-01

HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers. PMID:29755620

Energy transfer and color tunable emission in Tb3+,Eu3+ co-doped Sr3LaNa(PO4)3F phosphors.

PubMed

Li, Shuo; Guo, Ning; Liang, Qimeng; Ding, Yu; Zhou, Huitao; Ouyang, Ruizhuo; Lü, Wei

2018-02-05

A group of color tunable Sr 3 LaNa(PO 4 ) 3 F:Tb 3+ ,Eu 3+ phosphors were prepared by conventional high temperature solid state method. The phase structures, luminescence properties, fluorescence lifetimes and energy transfer were investigated in detail. Under 369nm excitation, owing to efficient energy transfer of Tb 3+ →Eu 3+ , the emission spectra both have green emission of Tb 3+ and red emission of Eu 3+ . An efficient energy transfer occur in Tb 3+ , Eu 3+ co-doped Sr 3 LaNa(PO 4 ) 3 F phosphors. The most possible mechanism of energy transfer is dipole-dipole interaction by Dexter's theoretical model. The energy transfer of Tb 3+ and Eu 3+ was confirmed by the variations of emission and excitation spectra and Tb 3+ /Eu 3+ decay lifetimes in Sr 3 LaNa(PO 4 ) 3 F:Tb 3+ ,Eu 3+ . The color tone can tuned from yellowish-green through yellow and eventually to reddish-orange with fixed Tb 3+ content by changing Eu 3+ concentrations. The results show that the prepared Tb 3+ , Eu 3+ co-doped color tunable Sr 3 LaNa(PO 4 ) 3 F phosphor can be used for white LED. Copyright © 2017 Elsevier B.V. All rights reserved.