ALBERT

Description: Background: This study compares Mycobacterium tuberculosis culture isolation and drug sensitivity testing (DST) using solid (LJ) and liquid (BACTEC-MGIT-960) media in Nigeria. Methods: This was a cross sectional survey of adults attending reference centres in Abuja, Ibadan and Nnewi with a new diagnosis of pulmonary tuberculosis (TB) or having failed the first-line TB treatment. Patients were requested to provide three sputum specimens for smear-microscopy and culture on LJ and BACTEC-MGIT-960. Positive cultures underwent DST for streptomycin, isoniazid, rifampicin and ethambutol. Results: 527 specimens were cultured. 428 (81%) were positive with BACTEC-MGIT-960, 59 (11%) negative, 36 (7%) contaminated and 4 (1%) had non-tuberculosis mycobacteria (NTM). 411 (78%) LJ cultures were positive, 89 (17%) negative, 22 (4%) contaminated and 5 (1%) had NTM. The mean (SD) detection time was 11 (6) and 30 (11) days for BACTEC-MGIT-960 and LJ. DST patterns were compared in the 389 concordant positive BACTEC-MGIT-960 and LJ cultures. Rifampicin and isoniazid DST patterns were similar. Streptomycin resistance was detected more frequently with LJ than BACTEC-MGIT-960 and ethambutol resistance was detected more frequently with BACTEC-MGIT-960 than LJ, but differences were not statistically significant. MDR-TB was detected by 27 cases by LJ and 25 by BACTEC-MGIT-960 and using both methods detected 29 cases. Conclusions: There was a substantial degree of agreement between the two methods. However using the two in tandem increased the number of culture-positive patients and with MDR-TB. The choice of culture method should depend on local availability, cost and test performance characteristics.

Description: Background: Respiratory disease can impose a significant burden on the health of rural populations. The Saskatchewan Rural Health Study (SRHS) is a new large prospective cohort study of ages 6 and over currently being conducted in farming and non-farming communities to evaluate potential health determinants associated with respiratory outcomes in rural populations. In this article, we describe the rationale and methodology for the adult component. Methods: The study is being conducted over 5 years (2009-15) in two phases, baseline and longitudinal. The baseline survey consists of two components, adults and children. The adult component consists of a questionnaire-based evaluation of individual and contextual factors of importance to respiratory health in two sub populations (a Farm Cohort and a Small Town Cohort) of rural families in Saskatchewan Rural Municipalities (RMs). Clinical studies of lung function and allergy tests are being conducted on selected sub-samples of the two cohorts based on the positive response to the last question on the baseline questionnaire: "Would you be willing to be contacted about having breathing and/or allergy tests at a nearby location?". We adopted existing population health theory to evaluate individual factors, contextual factors, and principal covariates on the outcomes of chronic bronchitis, chronic obstructive pulmonary disease, asthma and obstructive sleep apnea.FindingsOf the RMs selected to participate, 32 (89%) out of 36 RMs and 15 (94%) out of 16 small towns within the RMs agreed to participate. Using the mail out survey method developed by Dillman, we obtained completed questionnaires from 4264 households (8261 individuals). We obtained lung function measurements on 1609 adults, allergy skin test information on 1615 adults; both measurements were available on 1549 adults. We observed differences between farm and non-farm rural residents with respect to individual, contextual factors and covariates.DiscussionThere are differences between farm and non-farm rural residents with respect to individual and contextual factors and other variables of importance. The findings of the SRHS will improve knowledge of respiratory disease etiology, assist in the development and targeting of prevention programs, and in planning health services with farm and small town populations.

Description: Background: Multiple viruses, including human immunodeficiency virus, Epstein Barr virus (EBV) and mouse mammary tumour virus have been identified in human milk. High risk human papillomavirus (HPV) sequences have been identified in breast cancer. The aim of this study is to determine if viral sequences are present in human milk from normal lactating women.FindingsStandard (liquid) and in situ polymerase chain reaction (PCR) techniques were used to identify HPV and EBV in human milk samples from normal lactating Australian women who had no history of breast cancer.High risk human papillomavirus was identified in milk samples of 6 of 40 (15%) from normal lactating women - sequencing on four samples showed three were HPV 16 and one was HPV 18. Epstein Barr virus was identified in fourteen samples (33%). Conclusion: The presence of high risk HPV and EBV in human milk suggests the possibility of milk transmission of these viruses. However, given the rarity of viral associated malignancies in young people, it is possible but unlikely, that such transmission is associated with breast or other cancers.

Description: Background: Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumesin the semi-arid tropics. While most domesticated forms of cowpea are susceptible to the rootparasitic weed Striga gesnerioides, several cultivars have been identified that show racespecificresistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S.gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots ofcultivar B301 develop a strong resistance response characterized by a hypersensitive reactionand cell death at the site of parasite attachment. In contrast, no visible response occurs inB301 roots parasitized by SG4z. Results: Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) andincompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively,were investigated at the early (6 days post-inoculation (dpi)) and late (13 dpi) stages of theresistance response using a Nimblegen custom design cowpea microarray. A total of 111genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed duringcompatible (susceptible) interactions of B301 with SG4z . Genes and pathways involved insignal transduction, programmed cell death and apoptosis, and defense response to biotic andbiotic stress were differentially expressed in the early resistance response; at the later timepoint, enrichment was primarily for defense-related gene expression, and genes encodingcomponents of lignifications and secondary wall formation. In compatible interactions (B301- SG4z), multiple defense pathways were repressed, including those involved in ligninbiosynthesis and secondary cell wall modifications, while cellular transport processes fornitrogen and sulfur were increased. Conclusion: Distinct changes in global gene expression profiles occur in host roots following successfuland unsuccessful attempted parasitism by Striga. Induction of specific defense related genesand pathways defines components of a unique resistance mechanism. Some genes andpathways up-regulated in the host resistance response to SG3 are repressed in the susceptibleinteractions, suggesting that the parasite is targeting specific components of the host'sdefense. These results add to our understanding of plant-parasite interactions and theevolution of resistance to parasitic weeds.

Description: Background: Only a small fraction of the mosquito species of the genus Anopheles are able to transmit malaria, one of the biggest killer diseases of poverty, which is mostly prevalent in the tropics. This diversity has genetic, yet unknown, causes. In a further attempt to contribute to the elucidation of these variances, the international "Anopheles Genomes Cluster Consortium" project (a.k.a. "16 Anopheles genomes project") was established, aiming at a comprehensive genomic analysis of several anopheline species, most of which are malaria vectors. In the frame of the international consortium carrying out this project our team studied the genes encoding families of non-coding RNAs (ncRNAs), concentrating on four classes: microRNA (miRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and in particular small nucleolar RNA (snoRNA) and, finally, transfer RNA (tRNA). Results: Our analysis was carried out using, exclusively, computational approaches, and evaluating both the primary NGS reads as well as the respective genome assemblies produced by the consortium and stored in VectorBase; moreover, the results of RNAseq surveys in cases in which these were available and meaningful were also accessed in order to obtain supplementary data, as were "pre-genomic era" sequence data stored in nucleic acid databases. The investigation included the identification and analysis, in most species studied, of ncRNA genes belonging to several families, as well as the analysis of the evolutionary relations of some of those genes in cross-comparisons to other members of the genus Anopheles. Conclusions: Our study led to the identification of members of these gene families in the majority of twenty different anopheline taxa. A set of tools for the study of the evolution and molecular biology of important disease vectors has, thus, been obtained.

Description: Background: Most fishes possess two paralogs for myostatin, a muscle growth inhibitor, while salmonidsare presumed to have four: mstn1a, mstn1b, mstn2a and mstn2b, a pseudogene. Themechanisms responsible for preserving these duplicates as well as the depth of mstn2bnonfunctionalization within the family remain unknown. We therefore characterized severalgenomic clones in order to better define species and gene phylogenies. Results: Gene organization and sequence conservation was particularly evident among paraloggroupings and within salmonid subfamilies. All mstn2b sequences included in-frame stopcodons, confirming its nonfunctionalization across taxa, although the indels andpolymorphisms responsible often differed. For example, the specific indels within theOnchorhynchus tshawytscha and O. nerka genes were remarkably similar and differedequally from other mstn2b orthologs. A phylogenetic analysis weakly established a mstn2bclade including only these species, which coupled with a shared 51 base pair deletion mightsuggest a history involving hybridization or a shared phylogenetic history. Furthermore,mstn2 introns all lacked conserved splice site motifs, suggesting that the tissue-specificprocessing of mstn2a transcripts, but not those of mstn2b, is due to alternative cis regulationand is likely a common feature in salmonids. It also suggests that limited transcriptprocessing may have contributed to mstn2b nonfunctionalization. Conclusions: Previous studies revealed divergence within gene promoters while the current studies provideevidence for relaxed or positive selection in some coding sequence lineages. These resultstogether suggest that the salmonid myostatin gene family is a novel resource for investigatingmechanisms that regulate duplicate gene fate as paralog specific differences in geneexpression, transcript processing and protein structure are all suggestive of active divergence.

Description: Background: Cannibalism is widespread in both vertebrates and invertebrates but its extent is variable between and within species. Cannibalism depends on population density and nutritional conditions, and could be beneficial during colonisation of new environments. Empirical studies are needed to determine whether this trait might facilitate invasion of a new area in natural systems. We investigated whether the propensity for cannibalism in H. axyridis differs both between native and invasive populations and between invasive populations from the core and from the front of the invasive area in Western Europe. We also compared the propensity for cannibalism of these natural populations with that of laboratory-reared biocontrol populations. We measured the cannibalism rates of eggs by first instar larvae and adult females at two different individual densities of ladybirds from three types of population (invasive, native and biocontrol), in laboratory-controlled conditions. Results: Cannibalism was significantly greater in larvae from invasive populations compared to native or biocontrol populations, but there was no difference in cannibalism rates between populations from the core or front of the invaded range. Cannibalism was significantly lower in larvae from biocontrol populations compared to wild (invasive and native) populations. No differences in cannibalism rates of adult females were found between any populations. While high population density significantly increased cannibalism in both larvae and adults, the norm of reaction of cannibalism to individual density did not change significantly during the invasion and/or laboratory rearing processes. Conclusion: This study is the first to provide evidence for a higher propensity for cannibalism in invasive populations compared to native ones. Our experiments also shed light on the difference in cannibalism evolution with respect to life stages. However, we are still at an early stage in understanding the underlying mechanisms and several different research perspectives are needed to determine whether the higher propensity for cannibalism is a general feature of the invasion process.

Description: Background: Antimicrobial resistance is increasing among clinical Campylobacter cases and is common among isolates from other sources, specifically retail poultry - a major source of human infection. In this study the antimicrobial susceptibility of isolates from a UK-wide survey of Campylobacter in retail poultry in 2001 and 2004--5 was investigated. The occurrence of phenotypes resistant to tetracycline, quinolones (ciprofloxacin and naladixic acid), erythromycin, chloramphenicol and aminoglycosides was quantified. This was compared with a phylogeny for these isolates based upon Multi Locus Sequence Typing (MLST) to investigate the pattern of antimicrobial resistance acquisition. Results: Antimicrobial resistance was present in all lineage clusters, but statistical testing showed a non-random distribution. Erythromycin resistance was associated with Campylobacter coli. For all antimicrobials tested, resistant isolates were distributed among relatively distant lineages indicative of widespread acquisition. There was also evidence of clustering of resistance phenotypes within lineages; indicative of local expansion of resistant strains. Conclusions: These results are consistent with the widespread acquisition of antimicrobial resistance among chicken associated Campylobacter isolates, either through mutation or horizontal gene transfer, and the expansion of these lineages as a proportion of the population. As Campylobacter are not known to multiply outside of the host and long-term carriage in humans is extremely infrequent in industrialized countries, the most likely location for the proliferation of resistant lineages is in farmed chickens.

Description: Background: The perennial species Rhazya stricta (R. stricta) grows in arid zones and carries out typical C3 photosynthesis under daily extremes of heat, light intensity and low humidity. In order to identify processes attributable to its adaptation to this harsh environment, we profiled the foliar transcriptome of apical and mature leaves harvested from the field at three time periods of the same day. Results: Next generation sequencing was used to reconstruct the transcriptome and quantify gene expression. 28018 full length transcript sequences were recovered and 45.4% were differentially expressed (DE) throughout the day. We compared our dataset with microarray experiments in Arabidopsis thaliana (Arabidopsis) and other desert species to identify trends in circadian and stress response profiles between species. 34% of the DE genes were homologous to Arabidopsis circadian-regulated genes. Independent of circadian control, significant overlaps with Arabidopsis genes were observed only with heat and salinity/high light stress-responsive genes. Also, groups of DE genes common to other desert plants species were identified. We identified protein families specific to R. stricta which were found to have diverged from their homologs in other species and which were over -expressed at midday. Conclusions: This study shows that temporal profiling is essential to assess the significance of genes apparently responsive to abiotic stress. This revealed that in R.stricta, the circadian clock is a major regulator of DE genes, even of those annotated as stress-responsive in other species. This may be an important feature of the adaptation of R. stricta to its extreme but predictable environment. However, the majority of DE genes were not circadian-regulated. Of these, some were common to other desert species and others were distinct to R.stricta, suggesting that they are important for the adaptation of such plants to arid environments.