Tuberculosis in HIV-infected individuals in Ho Chi Minh City, Vietnam

Early and accurate detection of TB disease in HIV-infected individuals is a critical step for a successful TB program. In Vietnam, the diagnosis of TB disease, which is based predominantly on the clinical examination, chest radiography (CXR) and acid fast bacilli (AFB) sputum smear, has shown to be of low sensitivity in immunocompromised patients. The sputum culture is not routinely performed for patients with AFB negative smears, even in HIV-infected individuals.^ In that background, we conducted this cross-sectional study to estimate the prevalence of sputum culture-confirmed pulmonary tuberculosis (PTB), smear-negative PTB, and multidrug-resistant TB (MDR-TB) in the HIV-infected population in Ho Chi Minh City (HCMC), the largest city in Vietnam where both TB and HIV are highly prevalent. We also evaluated the diagnostic performance of various algorithms based on routine available tools in Vietnam such as symptoms screening, CXR, and AFB smear. Nearly 400 subjects were consecutively recruited from HIV-infected patients seeking care at the An Hoa Clinic in District 6 of Ho Chi Minh City from August 2009 through June 2010. Participants’ demographic data, clinical status, CXR, and laboratory results were collected. A multiple logistic regression model was developed to assess the association of covariates and PTB. ^ The prevalence of smear-positive TB, smear-negative TB, resistant TB, and MDR-TB were 7%, 2%, 5%, 2.5%, and 0.3%, respectively. Adjusted odds ratios for low CD4+ cell count, positive sputum smear, and CXR to positive sputum culture were 3.17, 32.04, and 4.28, respectively. Clinical findings alone had poor sensitivity, but the combination of CD4+ cell count, sputum smear, and CXR proved to perform a more accurate diagnosis.^ This study results support the routine use of sputum culture to improve the detection of TB disease in HIV-infected individuals in Vietnam. When routine sputum culture is not available, an algorithm combining CD4+ cell count, sputum smear, and CXR is recommended for diagnosing PTB. Future studies on more affordable, rapid, and accurate tests for TB infection would also be necessary to timely provide specific treatments for patients in need, reduce mortality, and minimize TB transmission to the general population.^

Targeted Deletion Of Functionally Validated Enhancers Defines Their Role in Mouse Limb Development

Transcriptional enhancers are genomic DNA sequences that contain clustered transcription factor (TF) binding sites. When combinations of TFs bind to enhancer sequences they act together with basal transcriptional machinery to regulate the timing, location and quantity of gene transcription. Elucidating the genetic mechanisms responsible for differential gene expression, including the role of enhancers, during embryological and postnatal development is essential to an understanding of evolutionary processes and disease etiology. Numerous methods are in use to identify and characterize enhancers. Several high-throughput methods generate large datasets of enhancer sequences with putative roles in embryonic development. However, few enhancers have been deleted from the genome to determine their roles in the development of specific structures, such as the limb. Manipulation of enhancers at their endogenous loci, such as the deletion of such elements, leads to a better understanding of the regulatory interactions, rules and complexities that contribute to faithful and variant gene transcription – the molecular genetic substrate of evolution and disease. To understand the endogenous roles of two distinct enhancers known to be active in the mouse embryo limb bud we deleted them from the mouse genome. I hypothesized that deletion of these enhancers would lead to aberrant limb development. The enhancers were selected because of their association with p300, a protein associated with active transcription, and because the human enhancer sequences drive distinct lacZ expression patterns in limb buds of embryonic day (E) 11.5 transgenic mice. To confirm that the orthologous mouse enhancers, mouse 280 and 1442 (M280 and M1442, respectively), regulate expression in the developing limb we generated stable transgenic lines, and examined lacZ expression. In M280-lacZ mice, expression was detected in E11.5 fore- and hindlimbs in a region that corresponds to digits II-IV. M1442-lacZ mice exhibited lacZ expression in posterior and anterior margins of the fore- and hindlimbs that overlapped with digits I and V and several wrist bones. We generated mice lacking the M280 and M1442 enhancers by gene targeting. Intercrosses between M280 -/+ and M1442 -/+, respectively, generated M280 and M1442 null mice, which are born at expected Mendelian ratios and manifest no gross limb malformations. Quantitative real-time PCR of mutant E11.5 limb buds indicated that significant changes in transcriptional output of enhancer-proximal genes accompanied the deletion of both M280 and M1442. In neonatal null mice we observed that all limb bones are present in their expected positions, an observation also confirmed by histology of E18.5 distal limbs. Fine-scale measurement of E18.5 digit bone lengths found no differences between mutant and control embryos. Furthermore, when the developmental progression of cartilaginous elements was analyzed in M280 and M1442 embryos from E13.5-E15.5, transient development defects were not detected. These results demonstrate that M280 and M1442 are not required for mouse limb development. Though M280 is not required for embryonic limb development it is required for the development and/or maintenance of body size – adult M280 mice are significantly smaller than control littermates. These studies highlight the importance of experiments that manipulate enhancers in situ to understand their contribution to development.

Spectral reflectance library of selected biotic and abiotic coral reef features in Glovers Reef, Belize

Underwater spectral reflectance was measured for selected biotic and abiotic coral reef features of Glovers Reef, Belize from March 6 - 10, 2005. Spectral reflectance's of 63 different benthic types were obtained in-situ. An Ocean Optics USB2000 spectrometer was deployed in an custom made underwater housing with a 0.5 m fiber-optic probe mounted next to an artificial light source. Spectral readings were collected with the probe (bear fibre) about 5 cm from the target to ensure that the target would fill the field of view of the fiber optic (FOV diameter ~4.4 cm), as well as to reduce the attenuating effect of the intermediate water (Roelfsema et al., 2006). Spectral readings included for one target included: 1 reading of the covered spectral fibre to correct for instrument noise, 1 reading of spectralon panel mounted on divers wrist to measure incident ambient light, and 8 readings of the target. Spectral reflectance was calculated for each target by first subtracting the instrument noise reading from each other reading. The corrected target readings were then divided by the corrected spectralon reading resulting in spectral reflectance of each target reading. An average target spectral reflectance was calculated by averaging the eight individual spectral reflectance's of the target. If an individual target spectral reflectance was visual considered an outlier, it was not included in the average spectral reflectance calculation. See Roelfsema at al. (2006) for additional info on the methodology of underwater spectra collection.

Animation of micro-computed tomography of bioerosion trace Entobia megastoma made by East Australian bioeroding sponge Cliona celata

Endolithic bioerosion is difficult to analyse and to describe, and it usually requires damaging of the sample material. Sponge erosion (Entobia) may be one of the most difficult to evaluate as it is simultaneously macroscopically inhomogeneous and microstructurally intricate. We studied the bioerosion traces of the two Australian sponges Cliona celata Grant, 1826 (sensu Schönberg 2000) and Cliona orientalis Thiele, 1900 with a newly available radiographic technology: high resolution X-ray micro-computed tomography (MCT). MCT allows non-destructive visualisation of live and dead structures in three dimensions and was compared to traditional microscopic methods. MCT and microscopy showed that C. celata bioerosion was more intense in the centre and branched out in the periphery. In contrast, C. orientalis produced a dense, even trace meshwork and caused an overall more intense erosion pattern than C. celata. Extended pioneering filaments were not usually found at the margins of the studied sponge erosion, but branches ended abruptly or tapered to points. Results obtained with MCT were similar in quality to observations from transparent optical spar under the dissecting microscope. Microstructures could not be resolved as well as with e.g. scanning electron microscopy (SEM). Even though sponge scars and sponge chips were easily recognisable on maximum magnification MCT images, they lacked the detail that is available from SEM. Other drawbacks of MCT involve high costs and presently limited access. Even though MCT cannot presently replace traditional techniques such as corrosion casts viewed by SEM, we obtained valuable information. Especially for the possibility to measure endolithic pore volumes, we regard MCT as a very promising tool that will continue to be optimised. A combination of different methods will produce the best results in the study of Entobia.

Analysis of the iron oxide assemblages in the ANDRILL AND-1B drill core, Ross Sea, Antarctica

The AND-1B drill core recovered a 13.57 million year Miocene through Pleistocene record from beneath the McMurdo Ice Shelf in Antarctica (77.9°S, 167.1°E). Varying sedimentary facies in the 1285 m core indicate glacial-interglacial cyclicity with the proximity of ice at the site ranging from grounding of ice in 917 m of water to ice free marine conditions. Broader interpretation of climatic conditions of the wider Ross Sea Embayment is deduced from provenance studies. Here we present an analysis of the iron oxide assemblages in the AND-1B core and interpret their variability with respect to wider paleoclimatic conditions. The core is naturally divided into an upper and lower succession by an expanded 170 m thick volcanic interval between 590 and 760 m. Above 590 m the Plio-Pleistocene glacial cycles are diatom rich and below 760 m late Miocene glacial cycles are terrigenous. Electron microscopy and rock magnetic parameters confirm the subdivision with biogenic silica diluting the terrigenous input (fine pseudo-single domain and stable single domain titanomagnetite from the McMurdo Volcanic Group with a variety of textures and compositions) above 590 m. Below 760 m, the Miocene section consists of coarse-grained ilmenite and multidomain magnetite derived from Transantarctic Mountain lithologies. This may reflect ice flow patterns and the absence of McMurdo Volcanic Group volcanic centers or indicate that volcanic centers had not yet grown to a significant size. The combined rock magnetic and electron microscopy signatures of magnetic minerals serve as provenance tracers in both ice proximal and distal sedimentary units, aiding in the study of ice sheet extent and dynamics, and the identification of ice rafted debris sources and dispersal patterns in the Ross Sea sector of Antarctica.

Chemical and mineral compositions of sedimentary deposits and magmatic rocks from DSDP Legs 41, 45, 48, and 49

This collective monography by a group of lithologists from the Geological Institute of the USSR Academy of Sciences summarizes materials of the Deep-Sea Drilling Project from the Atlantic Ocean. It gives results of processing materials on the sequences drilled during DSDP Legs 41, 45, 48 and 49. These studies were based on lithological-facial analysis combined with detailed mineralogical-petrographic description. Its chapters give a number of ideas on formation of the Earth sedimentary cover, which can be used for compilation of regional and global schemes of ocean paleogeography, reconstruction of history of some structures in the World Ocean, correlation between sedimentary processes on continents and in oceans, estimation of perspectives for oil and gas fields and ore formation.

Spectral reflectance library of selected biotic and abiotic coral reef features in Heron Reef

Underwater spectral reflectance was measured for selected biotic and abiotic coral reef features of Heron Reef from June 25-30, 2006. Spectral reflectance's of 105 different benthic types were obtained in-situ. An Ocean Optics USB2000 spectrometer was deployed in an custom made underwater housing with a 0.5 m fiber-optic probe mounted next to an artificial light source. Spectral readings were collected with the probe(bear fibre) about 5 cm from the target to ensure that the target would fill the field of view of the fiber optic (FOV diameter ~4.4 cm), as well as to reduce the attenuating effect of the intermediate water (Roelfsema et al., 2006). Spectral readings included for one target included: 1 reading of the covered spectral fibre to correct for instrument noise, 1 reading of spectralon panel mounted on divers wrist to measure incident ambient light, and 8 readings of the target. Spectral reflectance was calculated for each target by first subtracting the instrument noise reading from each other reading. The corrected target readings were then divided by the corrected spectralon reading resulting in spectral reflectance of each target reading. An average target spectral reflectance was calculated by averaging the eight individual spectral reflectance's of the target. If an individual target spectral reflectance was visual considered an outlier, it was not included in the average spectral reflectance calculation. See Roelfsema at al. (2006) for additional info on the methodology of underwater spectra collection.

(Table 1) Results of X-ray radiographic analyses of authigenic phosphorites from the Southwest Africa shelf

In the biologically productive area on the Southwest Africa shelf a current process of diagenetic phosphorite formation occurs. Remains of phytoplankton are the main source of phosphorus in host bottom sediments. Phosphorus concentrates in nodules due to its redistribution in bottom sediments and precipitation from interstitial waters. Accumulation of the phosphate nodules, as well as of scattered fish bone debris in sediments occurs at sudden change in hydrological conditions and removal of fine sediment fractions due to increased bottom currents or during transgressions.