Fabricated germanium-doped optical fibres for computed tomography dosimetry: Glow curve characteristics

Fabricated germanium (Ge)-doped optical fibre glow curve characteristics are investigated with respect to computed tomography (CT) dosimetry. 2.3 mol% and 6 mol% Ge-dopant concentration preforms have been used to produce flat and cylindrical fibres (FF and CF) of various size and diameter. The fibres are irradiated to doses of 20, 30 and 40 mGy for each of the beam qualities RQT 8 (100 kV), RQT 9 (120 kV) and RQT 10 (150 kV). The thermoluminescence (TL) kinematic parameters studied are maximum temperature (Tmax), activation energy (Ea) and peak integral (PI). The glow curve formations are reconstructed from the Windows®–based radiation evaluation and management system (WinREMS), deconvoluted using glow curve deconvolution (CGCD) analysis software. The structures of the glow curves are broad single or double-peaked, occurring at relatively high glow peak temperatures, TL response increases with radiation dose and peak height decreases with increasing energy, showing clear photoelectric dependence. The deconvoluted glow curves for all fibres are seen to consist of five individual glow peaks, P1 to P5, P1 being dominant in all cases other than for 6 mol% Ge-FF for which P3 is dominant due to the formation of a double-peaked glow curve. Tmax increases from P1 to P5 for all fibres, throughout the energy range used. P1 and P3 (6 mol% Ge-FF) have the lowest Ea, while P4 shows the greatest Ea for all fibres. The results indicate that electrons in P1 and P3 (6 mol% Ge-FF) are occupied at low energy traps while for P4, the electrons are trapped at a deeper energy level. The lowest PI value, indicative of the least number of electrons, is shown to be that of the deeper trap P4 for all energies investigated. This study provides support for the use of 6 mol% and 2.3 mol% preform fibres for CT dosimetry, each with similar kinetic parameters

The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat

Extremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glaciozyma antarctica. The genome annotation identified 7857 protein coding sequences. From the genome sequence analysis we were able to identify genes that encoded for proteins known to be associated with cold survival, in addition to annotating genes that are unique to G. antarctica. For genes that are known to be involved in cold adaptation such as anti-freeze proteins (AFPs), our gene expression analysis revealed that they were differentially transcribed over time and in response to different temperatures. This indicated the presence of an array of adaptation systems that can respond to a changing but persistent cold environment. We were also able to validate the activity of all the AFPs annotated where the recombinant AFPs demonstrated anti-freeze capacity. This work is an important foundation for further collective exploration into psychrophilic microbiology where among other potential, the genes unique to this species may represent a pool of novel mechanisms for cold survival

Measuring Data Completeness for Microbial Genomics Database

Poor quality data such as data with missing values (or records) cause negative consequences in many application domains. An important aspect of data quality is completeness. One problem in data completeness is the problem of missing individuals in data sets. Within a data set, the individuals refer to the real world entities whose information is recorded. So far, in completeness studies however, there has been little discussion about how missing individuals are assessed. In this paper, we propose the notion of population-based completeness (PBC) that deals with the missing individuals problem, with the aim of investigating what is required to measure PBC and to identify what is needed to support PBC measurements in practice. This paper explores the need of PBC in the microbial genomics where real sample data sets retrieved from a microbial database called Comprehensive Microbial Resources are used (CMR).</p

A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1

Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes

Unravelling the consequences of the bacteriophages in human samples

Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs