The Asian fish tapeworm (Schyzocotyle acheilognathi) is an important fish parasite with a wide host range that infects over 300 species of fish worldwide. Schyzocotyle acheilognathi has been reported from eastern coastal areas of Australia, but has not been previously reported in Western Australia (WA). During a control program for invasive freshwater fishes in south-western WA, a region with a unique and highly endangered freshwater fish fauna, tapeworms identified as S. acheilognathi from their distinctive scolex morphology were found at a prevalence of 3.3% in goldfish (Carassius auratus), 37.0% in koi carp (Cyprinus carpio haematopterus) and 65.0% in eastern gambusia (Gambusia holbrooki) in a small suburban lake to the north of Perth. For molecular confirmation, the 18S ribosomal RNA gene was targeted at hypervariable V4 region. Koi carp isolates were 100% identical to S. acheilognathi isolated from varying hosts, including the red shiner (Cyprinella lutrensis) and a human sample. Sequences obtained from two eastern gambusia were identified as S. acheilognathi, but formed a discrete cluster and may represent a novel genotype. Isolates from two other eastern gambusia and two goldfish formed a distinct clade with only 91.9% similarity to previously sequenced isolates of S. acheilognathi. This emphasizes the importance of molecular identification methods in addition to morphological identification. The presence and potential for transmission of these parasites in south-western WA may threaten the health of native fishes, which are immunologically naïve to this introduced parasite. Immediate control or containment measures should be implemented to halt the spread of these parasites.

Influenza is a major human respiratory pathogen. Due to the high levels of influenza-like illness (ILI) in Zhejiang, China, the control and prevention of influenza was challenging during the 2017–2018 season. To identify the clinical spectrum of illness related to influenza and characterise the circulating influenza virus strains during this period, the characteristics of ILI were studied. Viral sequencing and phylogenetic analyses were conducted to investigate the virus types, substitutions at the amino acid level and phylogenetic relationships between sequences. This study has shown that the 2017/18 influenza season was characterised by the co-circulation of influenza A (H1N1) pdm09, A (H3N2) and B viruses (both Yamagata and Victoria lineage). From week 36 of 2017 to week 12 of 2018, ILI cases accounted for 5.58% of the total number of outpatient and emergency patient visits at the surveillance sites. Several amino acid substitutions were detected. Vaccination mismatch may be a potential reason for the high percentage of ILI. Furthermore, it is likely that multiple viral introductions played a role in the endemic co-circulation of influenza in Zhejiang, China. More detailed information regarding the molecular epidemiology of influenza should be included in long-term influenza surveillance.

The springtail Megalothorax laevis Denis, 1948 is redescribed from a broad sampling in the intertropical zone: Vietnam (including type locality), Ivory Coast, Gabon, Réunion island and French Guiana. Pseudopore-like elements are for the first time reported on the trunk and legs of Megalothorax species. New molecular data for M. laevis (16S rDNA, 28S rDNA d1 and d2 and COI Barcode) are provided. The phylogenetic position of the species within the Megalothorax genus is analysed. Megalothorax laevis belongs to the incertus group but shares similitudes with the minimus group acquired through evolutionary convergences (such as smooth lamellae of the mucro). Those similitudes might have created confusion between M. minimus and M. laevis. While M. minimus used to be regarded cosmopolitan, M. laevis has been overlooked since its original discovery. However, the present sampling led us to believe that M. laevis replace M. minimus as the commonest edaphic Megalothorax species in the intertropical zone. A key to the Megalothorax species with smooth mucro lamellae is provided.

Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. The findings of this study reveal significant morphological variation among African tomato contributed by plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (HO=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (HO=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (Fst) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.

The emergence of human and animal rabies in Bali since November 2008 has attracted local, national and international interest. The potential origin and time of introduction of rabies virus to Bali is described. The nucleoprotein (N) gene of rabies virus from dog brain and human clinical specimens was sequenced using an automated DNA sequencer. Phylogenetic inference with Bayesian Markov Chain Monte Carlo (MCMC) analysis using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) v. 1.7.5 software confirmed that the outbreak of rabies in Bali was caused by an Indonesian lineage virus following a single introduction. The ancestor of Bali viruses was the descendant of a virus from Kalimantan. Contact tracing showed that the event most likely occurred in early 2008. The introduction of rabies into a large unvaccinated dog population in Bali clearly demonstrates the risk of disease transmission for government agencies and should lead to an increased preparedness and efforts for sustained risk reduction to prevent such events from occurring in future.

Pomacanthidae is a family of coral reef fish that consists of approximately 74 species. Ten species of these fish have been identified in the Persian Gulf, one of them being yellow-bar angelfish (Pomacanthus maculosus). The phylogenetic relationship of these fish was studied using 10 samples collected from three regions of Iran: Larak Island, Lengeh Port and Genaveh Port. To analyse mtDNA, 760 base pairs of the cytochrome b gene were amplified and sequenced. The target region of the mtDNA was amplified using the polymerase chain reaction (PCR) and then PCR products were analysed by the phylogenetic analyses of the DNA sequences based on Phylodraw and ClustalW software. Samples were aligned together and with other cytochrome b gene sequences of angelfish from GenBank. Comparison of the phylogenetic trees indicated that all samples belong to a monophyletic group, while comparison of the phylogenetic tree obtained from the cytochrome b gene of P. maculosus samples from the Persian Gulf and other angelfish in GenBank, showed that P. maculosus is closer to Pomacanthus semicirculatus and Pomacanthus imperator than other species of GenBank.

Phylogenetic analysis was performed on the haemagglutinin and neuraminidase subtype N2 genes of low-pathogenic avian influenza viruses (LPAIVs) detected in Ireland between 2003 and 2007. Nucleotide sequences were compared to previously published sequences from the National Centre for Biotechnology Information. Sequences from viruses of the same subtype isolated in different years were compared to examine the possibility that LPAIVs may have been maintained in Ireland from year to year. All viruses had closest identity with published sequences of European lineage, supporting the conclusion that LPAIVs had been introduced to Ireland by dabbling ducks that had migrated from Europe. The data suggested that different subtypes of virus had been introduced each year. However, there was evidence that some LPAIVs may have been maintained in the sedentary waterfowl population for consecutive seasons. Furthermore, almost identical H6 and H10 sequences with different N types were found in isolates from the same season, suggesting that reassortment had occurred.

Bangladesh first experienced highly pathogenic avian influenza (HPAI) in early 2007 and the National Reference Laboratory for Avian Influenza (NRL-AI) at BLRI diagnosed and confirmed the presence of H5 sub-type virus on 15 March 2007. Until May 2009, NRL-AI observed 323 H5 and three H9 positive cases. Gene sequencing of 25 isolates of 2007 and 2008 demonstrated 99.1 to 100% identical genetic structure, indicating a single introduction of the virus in Bangladesh. It also clearly demonstrated that Bangladeshi isolates belong to the sub-clade 2.2 popularly known as Qinghai lineage or Euro-Asian-African lineage with highest similarities to those from Kuwait, Mongolia, Russia and Afghanistan. The close similarities between the HPAI isolates of these countries with Bangladeshi isolates suggest that migratory birds might be responsible for initial introduction of HPAI in Bangladesh as the country has no poultry trade link with these countries. Identifying possible risk factors in the spread of HPAI in the country was examined through descriptive as well as case control studies. It was revealed that, in most cases, mortality in backyard chicken flocks preceded an outbreak on commercial farms. Poor management and breaches in biosecurity practices appeared to have significant role in the spread of HPAI. The poultry industry in Bangladesh faced a terrific financial loss in 2007 and 2008 due to the incursion of avian influenza, which was estimated to be at Taka 3858 crore (38580 million). The prices of broiler declined by about 28% while the price of eggs decreased by 26.5%, as more than one third of consumers refrained from consumption of broiler meat and eggs. As a result of this market collapse, many farm owners were compelled to abandon poultry production because of loss of capital.

ABC systems are one of the largest described protein superfamilies. These systems have a domain organization that may contain 1 or more transmembrane domains (ABC_TM1F) and 1 or 2 ATP-binding domains (ABC_2). The functions (e.g., import, export and DNA repair) of these proteins distinguish the 3 classes of ABC systems. Mining and PCR-based cloning were used to identify 33 putative ABC systems from the Brugia malayi genome. There were 31 class 2 genes, commonly called ABC transporters, and 2 class 3 genes. The ABC transporters were divided into subfamilies. Three belonged to subfamily A, 16 to subfamily B, 5 to subfamily C, 1 to subfamily E and 3 to subfamilies F and G, respectively. None were placed in subfamilies D and H. Similar to other ABC systems, the ABC_2 domain of B. malayi genes was conserved and contained the Walker A and B motifs, the signature sequence/linker region and the switch region with the conserved histidine. The ABC_TM1F domain was less conserved. The relative abundance of ABC systems was quantified using real-time reverse transcription PCR and was significantly higher in female adults of B. malayi than in males and microfilaria, particularly those in subfamilies B and C, which are associated with drug resistance.

In an effort to minimize the probability of forward contamination of pristine extraterrestrial environments, the National Aeronautics and Space Administration requires that all US robotic spacecraft undergo assembly, testing and launch operations (ATLO) in controlled clean-room environments. This study examines the impact of ATLO activity on the microbial diversity and overall bioburden contained within the air of the clean-room facility in which the Mars Exploration Rovers (MERs) underwent final preparations for launch. Air samples were collected from several facility locations and traditional culture-based and molecular methodologies were used to measure microbial burden and diversity. Surprisingly, the greatest estimates of airborne bioburden, as derived from ATP content and cultivation assays, were observed prior to the commencement of MER ATLO activities. Furthermore, airborne microbial diversity gradually declined from the initiation of ATLO on through to launch. Proteobacterial sequences were common in 16S rDNA clone libraries. Conspicuously absent were members of the Firmicutes phylum, which includes the genus Bacillus. In previous studies, species of this genus were repeatedly isolated from the surfaces of spacecraft and clean-room assembly facilities. Increased cleaning and maintenance initiated immediately prior to the start of ATLO activity could explain the observed declines in both airborne bioburden and microbial diversity.

Evolutionary and closer structural relationships are demonstrated by phylogenetic analysis, peptide prediction and molecular modelling between Solanum tuberosum apyrase, Schistosoma mansoni SmATPase 2 and Leishmania braziliensis NDPase. Specific protein domains are suggested to be potentially involved in the immune response, and also seem to be conserved during host and parasite co-evolution. Significant IgG antibody reactivity was observed in sera from patients with American cutaneous leishmaniasis (ACL) and schistosomiasis using potato apyrase as antigen in ELISA. S. mansoni adult worm or egg, L. braziliensis promastigote (Lb) and Trypanosoma cruzi epimastigote (EPI) have ATP diphosphohydrolases, and antigenic preparations of them were evaluated. In ACL patients, IgG seropositivity was about 43% and 90% for Lb and potato apyrase, respectively, while IgM was lower (<19%) for both. In schistosomiasis patients IgM (>40%) or IgG (100%) seropositivity for both soluble egg (SEA) and adult worm (SWAP) antigens was higher than that found for potato apyrase (IgM=10%; IgG=39%). In Chagas disease, IgG seropositivity for EPI and potato apyrase was 97% and 17%, respectively, while the IgM was low (3%) for both antigens. The study of the conserved domains from both parasite proteins and potato apyrase could lead to the development of new drug targets or molecular markers.