Molecular epidemiology of respiratory viruses in a paediatric cohort from Indonesia

Acute lower respiratory tract infections (ALRTIs) are a common cause of morbidity and mortality among children under 5 years of age and are found worldwide, with pneumonia as the most severe manifestation. Although the incidence of severe disease varies both between individuals and countries, there is still no clear understanding of what causes this variation. Studies of community-acquired pneumonia (CAP) have traditionally not focused on viral causes of disease due to a paucity of diagnostic tools. However, with the emergence of molecular techniques, it is now known that viruses outnumber bacteria as the etiological agents of childhood CAP, especially in children under 2 years of age. The main objective of this study was to investigate viruses contributing to disease severity in cases of childhood ALRTI, using a two year cohort study following 2014 infants and children enrolled in Bandung, Indonesia. A total of 352 nasopharyngeal washes collected from 256 paediatric ALRTI patients were used for analysis. A subset of samples was screened using a novel microarray pathogen detection method that identified respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and human rhinovirus (HRV) in the samples. Real-time RT-PCR was used both for confirming and quantifying viruses found in the nasopharyngeal samples. Viral copy numbers were determined and normalised to the numbers of human cells collected with the use of 18S rRNA. Molecular epidemiology was performed for RSV A and hMPV using sequences to the glycoprotein gene and nucleoprotein gene respectively, to determine genotypes circulating in this Indonesian paediatric cohort. This study found that HRV (119/352; 33.8%) was the most common virus detected as the cause of respiratory tract infections in this cohort, followed by the viral pathogens RSV A (73/352; 20.7%), hMPV (30/352; 8.5%) and RSV B (12/352; 3.4%). Co-infections of more than two viruses were detected in 31 episodes (defined as an infection which occurred more than two weeks apart), accounting for 8.8% of the 352 samples tested or 15.4% of the 201 episodes with at least one virus detected. RSV A genotypes circulating in this population were predominantly GA2, GA5 and GA7, while hMPV genotypes circulating were mainly A2a (27/30; 90.0%), B2 (2/30; 6.7%) and A1 (1/30; 3.3%). This study found no evidence of disease severity associated either with a specific virus or viral strain, or with viral load. However, this study did find a significant association with co-infection of RSV A and HRV with severe disease (P = 0.006), suggesting that this may be a novel cause of severe disease.

Bioavailability of soil organic carbon and Fe as influenced by forestry practices in a subtropical coastal catchment

Potential impacts of plantation forestry practices on soil organic carbon and Fe available to microorganisms were investigated in a subtropical coastal catchment. The impacts of harvesting or replanting were largely limited to the soil top layer (0–10 cm depth). The thirty-year-old Pinus plantation showed low soil moisture content (Wc) and relatively high levels of soil total organic carbon (TOC). Harvesting and replanting increased soil Wc but reduced TOC levels. Mean dissolved organic carbon (DOC) and microbial biomass carbon (MBC) increased in harvested or replanted soils, but such changes were not statistically significant (P > 0.05). Total dithionite-citrate and aqua regia-extractable Fe did not respond to forestry practices, but acid ammonium oxalate and pyrophosphate-extractable, bioavailable Fe decreased markedly after harvesting or replanting. Numbers of heterotrophic bacteria were significantly correlated with DOC levels (P < 0.05), whereas Fe-reducing bacteria and S-bacteria detected using laboratory cultivation techniques did not show strong correlation with either soil DOC or Fe content.

Raman spectroscopic study of the antimonate mineral bottinoite Ni[Sb2(OH)12].6H2O and in comparison with brandholzite Mg[Sb5+2(OH)12]•6H2O

Raman spectra of bottinoite Ni[Sb(OH)6].6H2O were studied, and related to the molecular structure of the mineral. An intense sharp Raman band at 618 cm-1 is attributed to the SbO symmetric stretching mode. The low intensity band at 735 cm-1 is ascribed to the SbO antisymmetric stretching vibration. Low intensity Raman bands were found at 501, 516 and 578 cm-1. Four Raman bands observed at 1045, 1080, 1111 and 1163 cm-1 are assigned to δ SbOH deformation modes. A complex pattern resulting from the overlapping band of the water and hydroxyl units is observed. Raman bands are observed at 3223, 3228, 3368, 3291, 3458 and 3510 cm-1. The first two Raman bands are assigned to water stretching vibrations. The two higher wavenumber Raman bands observed at 3466 and 3552 cm-1 and two infrared bands at 3434 and 3565 cm-1 are assigned to the stretching vibrations of the hydroxyl units. Observed Raman and infrared bands are connected with O-H…O hydrogen bonds and their lengths 2.72, 2.79, 2.86, 2.88 and 3.0 Å (Raman) and 2.73, 2.83 and 3.07 Å (infrared).

Molecular characterisation of six badnavirus species associated with leaf streak disease of banana in East Africa

Banana leaf streak disease, caused by several species of Banana streak virus (BSV), is widespread in East Africa. We surveyed for this disease in Uganda and Kenya, and used rolling-circle amplification (RCA) to detect the presence of BSV in banana. Six distinct badnavirus sequences, three from Uganda and three from Kenya, were amplified for which only partial sequences were previously available. The complete genomes were sequenced and characterised. The size and organisation of all six sequences was characteristic of other badnaviruses, including conserved functional domains present in the putative polyprotein encoded by open reading frame (ORF) 3. Based on nucleotide sequence analysis within the reverse transcriptase/ribonuclease H-coding region of open reading frame 3, we propose that these sequences be recognised as six new species and be designated as Banana streak UA virus, Banana streak UI virus, Banana streak UL virus, Banana streak UM virus, Banana streak CA virus and Banana streak IM virus. Using PCR and species-specific primers to test for the presence of integrated sequences, we demonstrated that sequences with high similarity to BSIMV only were present in several banana cultivars which had tested negative for episomal BSV sequences.

Molecular analysis of the myosin gene family in Arabidopsis thaliana

Myosin is believed to act as the molecular motor for many actin-based motility processes in eukaryotes. It is becoming apparent that a single species may possess multiple myosin isoforms, and at least seven distinct classes of myosin have been identified from studies of animals, fungi, and protozoans. The complexity of the myosin heavy-chain gene family in higher plants was investigated by isolating and characterizing myosin genomic and cDNA clones from Arabidopsis thaliana. Six myosin-like genes were identified from three polymerase chain reaction (PCR) products (PCR1, PCR11, PCR43) and three cDNA clones (ATM2, MYA2, MYA3). Sequence comparisons of the deduced head domains suggest that these myosins are members of two major classes. Analysis of the overall structure of the ATM2 and MYA2 myosins shows that they are similar to the previously-identified ATM1 and MYA1 myosins, respectively. The MYA3 appears to possess a novel tail domain, with five IQ repeats, a six-member imperfect repeat, and a segment of unique sequence. Northern blot analyses indicate that some of the Arabidopsis myosin genes are preferentially expressed in different plant organs. Combined with previous studies, these results show that the Arabidopsis genome contains at least eight myosin-like genes representing two distinct classes.

A coupled meshless technique/molecular dynamics approach for deformation characterization of monocrystalline metal

This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M2) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M2, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic poentials and Cauchy-Born rule. The key parameters used in M2 are firstly investigated using a benchmark problem. Then M2 is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

Electron paramagnetic resonance, NIR studies on zoisite, clinozoisite and chrom-zoisite minerals

A zoisite group of mineral samples from different localities are used in the present study. An EPR study on powdered samples confirms the presence of Mn(II), Fe(III) and Cr(III) in the minerals. NIR studies confirm the presence of these ions in the minerals.

Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy

Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic diversity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic diversity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.

Engaging students in clinical bacteriology: A fresh look

Frequently there is a disconnectedness, either perceived or actual, between theoretical principles and laboratory practice in science education and this holds true for clinical microbiology where traditionally knowledge is delivered in ‘chunks’ in a lecture format with the misguided belief that students have to know ‘everything about everything’. This preoccupation with content delivery often leaves no time for active class discussion or reflection. Moreover, laboratory classes are treated as add-ons to the process, rather than an integrated part of the whole learning experience. In redesigning our units (subjects) we have bridged the gap between the theory and practice of clinical bacteriology. In doing so, we have seen a transformation in the learning experiences of our students and in the way we teach.

A polymorphism in the dysbindin gene (DTNBP1) associated with multiple psychiatric disorders including schizophrenia

Background A number of studies have found associations between dysbindin (DTNBP1) polymorphisms and schizophrenia. Recently we identified a DTNBP1 SNP (rs9370822) that is strongly associated with schizophrenia. Individuals diagnosed with schizophrenia were nearly three times as likely to carry the CC genotype compared to the AA genotype. Methods To investigate the importance of this SNP in the function of DTNBP1, a number of psychiatric conditions including addictive behaviours and anxiety disorders were analysed for association with rs9370822. Results The DTNBP1 polymorphism was significantly associated with post-traumatic stress disorder (PTSD) as well as nicotine and opiate dependence but not alcohol dependence. Individuals suffering PTSD were more than three times as likely to carry the CC genotype compared to the AA genotype. Individuals with nicotine or opiate dependence were more than twice as likely to carry the CC genotype compared to the AA genotype. Conclusions This study provides further support for the importance of DTNBP1 in psychiatric conditions and suggests that there is a common underlying molecular defect involving DTNBP1 that contributes to the development of several anxiety and addictive disorders that are generally recognised as separate clinical conditions. These disorders may actually be different expressions of a single metabolic pathway perturbation. As our participant numbers are limited our observations should be viewed with caution until they are independently replicated.

Molecular structure of Mg-Al, Mn-Al and Zn-Al halotrichites : an infrared spectroscopic study

Near infrared (NIR), X-ray diffraction (XRD) and infrared (IR) spectroscopy have been applied to halotrichites of the formula MgAl2(SO4)4∙22H2O, MnAl2(SO4)4∙22H2O and ZnAl2(SO4)4∙22H2O. Comparison of the halotrichites in different spectral regions has shown that the incorporation of a divalent transition metal into the halotrichite structure causes a shift in OH stretching band positions to lower wavenumbers. Therefore, an increase in hydrogen bonded water is observed for divalent cations with a larger molecular mass. XRD has confirmed the formation of halotrichite for all three samples and characteristic peaks of halotrichite have been identified at 18.5 and 24.5° 2θ, along with a group of six peaks between 5 and 15° 2θ. It has been observed that Mg-Al and Mn-Al halotrichite are very similar in structure, while Zn-Al showed several differences particularly in the NIR spectra. This work has shown that halotrichite structures can be synthesised and characterised by infrared and NIR spectroscopy.

Raman spectroscopic study of the uranyl titanate mineral brannerite (U,Ca,Y,Ce)2(Ti,Fe)2O6 –Effect of Metamictization

Raman spectra of the uranyl titanate mineral brannerite were analysed and related to the mineral structure. A comparison is made with the Raman spectra of uranyl oxyhydroxide hydrates. Observed bands are attributed to the TiO and (UO2)2+ stretching and bending vibrations, U-OH bending vibrations, H2O and (OH)- stretching, bending and libration modes. U-O bond lengths in uranyls and O-H…O bond lengths are calculated from the wavenumbers assigned to the stretching vibrations. Raman bands of brannerite are in harmony with those of the uranyl oxyhydroxides. The mineral brannerite is metamict as is evidenced by the intensity of the UO stretching and bending modes being of lower intensity than expected and with bands that are significantly broader.

Diversity of community acquired MRSA carrying the PVL gene in Queensland and New South Wales, Australia

Emergence and dissemination of community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains are being reported with increasing frequency in Australia and worldwide. These strains of CA-MRSA are genetically diverse and distinct in Australia. Genotyping of CA-MRSA using eight highly-discriminatory single nucleotide polymorphisms (SNPs) is a rapid and robust method for monitoring the dissemination of these strains in the community. In this study, a SNP genotyping method was used to investigate the molecular epidemiology of 249 community acquired non-multiresistant MRSA (nm-MRSA) isolates over a 12-month period from routine diagnostic specimens. A real-time PCR for the presence of Panton-Valentine leukocidin (PVL) was also performed on these isolates. The CA-MRSA isolates were sourced from a large private laboratory in Brisbane, Australia that serves a wide geographic region encompassing Queensland and Northern New South Wales. This study identified 16 different STs and 98% of the CA-MRSA isolates were positive for the PVL gene. The most common ST was ST93 with 41% of isolates testing positive for this clone.