Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus

Cyanophages play a crucial role in the biogeochemical cycles of aquatic ecosystems by affecting the population dynamics and community structure of cyanobacteria. In this study, a novel cyanophage, Nanhaivirus ms29, that infects Synechococcus sp. MW02 was isolated from the ocean basin in the South China Sea. It was identified as a T4-like phage using transmission electron microscopy. Phylogenetic analysis demonstrated that this cyanophage is distinct from other known T4-like cyanophage, belonging to a novel genus named Nanhaivirus within the family Kyanoviridae, according to the most recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV). The genome of this novel cyanophage is composed of 178,866 bp of double-stranded DNA with a G + C content of 42.5%. It contains 217 potential open reading frames (ORFs) and 6 tRNAs. As many as 30 auxiliary metabolic genes (AMGs) were identified in the genome, which related to photosynthesis, carbon metabolism, nutrient uptake and stress tolerance, possibly reflecting a genomic adaption to the oligotrophic environment. Read-mapping analysis showed that Nanhaivirus ms29 mainly distributed in temperate and tropical epipelagic waters. This study enriches of the virus gene database of cyanophages and provides valuable insights into the phylogeny of cyanophages and their interactions with their hosts

Characterization and Genome Sequence of Marine Alteromonas gracilis Phage PB15 Isolated from the Yellow Sea, China

A novel marine Alteromonas gracilis siphovirus, phage PB15, was isolated from the surface water of the Yellow Sea in August 2015. It has a head diameter of 58 ± 5 nm head and a contractile tail approximately 105 ± 10 nm in length, and overall the morphology suggests that PB15 belongs to the family Siphoviridae. PB15 phage is stable at over the temperature range 0-60oC. The best MOI of these phage was 0.1 and infectivity decreased above 60oC. The results suggest that phage is stable at pH value ranging between 3.0 and 11.0. Chloroform test shows that PB15 is not a lipid-containing phage. A one-step growth curve with a strain of A. gracilis gave a latent period of 16 minutes and rise period of 24 minutes and burst size of 60 PFU/cell. Genomic analysis of PB15 reveals a genome size of 37,333bp with 45.52% G+C content, and 61 ORFs. ORF sequences accounted for 30.36% of the genome sequence. There is no obvious similarity between PB15 and other known phages by genomic comparison using the BLASTN tool in the NCBI database

Characterization and genome analysis of Vibrio phage vB_VhaP_PG11, representing a new viral genus

Vibrio is a kind of common gram-negative bacteria, which is widely distributed in marine and estuarine environments. In the study, a novel marine phage vB_VhaP_PG11, infecting Vibrio hangzhouensis, was isolated from the offshore waters of Qingdao, China. vB_VhaP_PG11 is a double-stranded DNA phage. The whole genome proteomic tree shows that vB_VhaP_PG11 phage is related to two Vibrio phages, Vibrio phage 1.238.A._10N.261.52.F10 and Vibrio phage 1.245.O._10N.261.54.C7, but with low homology. Their amino acids identity with vB_VhaP_PG11 is 42.77 and 41.49% respectively. The prediction results of genome-blast distance phylogeny (GBDP) and the analysis gene-sharing network indicate that vB_VhaP_PG11 belongs to a new genus in Schitoviridae, named Qingschitovirus. The study of Vibrio phage vB_VhaP_PG11 provides basic information contributing to a better understanding of interactions between Vibrio phages and their hosts and helps analyze unknown viral sequences in the metagenomic database

Epidemiology of anti-tuberculosis drug resistance in a chinese population: current situation and challenges ahead

<p>Abstract</p> <p>Background</p> <p>Drug resistance has been a cause of concern for tuberculosis (TB) control in both developed and developing countries. Careful monitoring of the patterns and trends of drug resistance should remain a priority.</p> <p>Methods</p> <p>Strains were collected from 1824 diagnosed sputum smear positive pulmonary TB patients in Jiangsu province of China and then tested for drug susceptibility against rifampicin, isoniazid, ethambutol and streptomycin. The prevalence and patterns of drug resistance in mycobacterium tuberculosis (MTB) isolates were investigated. Multiple logistic regression analysis was performed to identify the risk factors for multidrug resistant (MDR) bacterial infection. The strength of association was estimated by odds ratio (OR) and 95% confidence interval (95% CI).</p> <p>Results</p> <p>The drug susceptibility tests showed that 1077(59.05%) MTB strains were sensitive to all the four antibiotics and the other 747(40.95%) strains were resistant to at least one drug. The proportions of mono-drug resistance were 28.73% for isoniazid, 19.41% for rifampicin, 29.33% for streptomycin, and 13.98% for ethambutol, respectively. The prevalence of MDR-TB was 16.61%, which was significantly different between new cases (7.63%) and those with previous treatment history (33.07%). Geographical variation of drug resistance was observed, where the proportion of MDR-TB among new cases was higher in the central (9.50%) or north part (9.57%) than that in the south area (4.91%) of Jiangsu province. The age of patients was significantly associated with the risk of drug resistance (P < 0.001) and the adjusted OR (95% CI) was 1.88(1.26-2.81) for patients aged 35-44 years when compared with those 65 years or older. Patients with previous treatment history had a more than 5-fold increased risk of MDR-TB (adjusted OR: 6.14, 95% CI: 4.61-8.17), compared with those previously not having been treated.</p> <p>Conclusions</p> <p>The high prevalence of drug resistance has been a major challenge for TB control. Prevention and control of drug-resistant TB should be emphasized by the revised DOTS (direct observed therapy, short course) program through prompt case detection, routine and quality-assured drug susceptibility test for patients at high risk of resistance, programmatic treatment with both first and second-line medicines, and systematic treatment observation, with priority for high MDR-TB settings.</p

Comparative study of the composition and genetic diversity of the picoeukaryote community in a Chinese aquaculture area and an open sea area

Picoeukaryotes (<2–3 μm) perform key roles for the functioning of marine ecosystems, but little is known regarding the composition and diversity of picoeukaryotes in aquaculture areas. In this study, the Illumina MiSeq platform was used for sequencing the V4 variable region within the 18S rDNA gene to analyse genetic diversity and relative abundance of picoeukaryotic communities in the Qinhuangdao scallop cultivation area of the Bohai Sea. The community was dominated by three super groups, the alveolates (54%), stramenopiles (41%) and chlorophytes (3%), and three groups, dinoflagellates (54%), pelagomonadales (40%) and prasinophytes (3%). Furthermore, a contrasting station with open water away from the eutrophic aquaculture area was chosen. The communities collected from the two stations exhibited significant differences, with higher diversity in the aquaculture area. These results provide the first snapshot of the picoeukaryotic diversity in surface waters of the Qinhuangdao scallop cultivation area, and basic data for future studies on picoeukaryote community in an aquaculture region

Viral Diversity and Its Relationship With Environmental Factors at the Surface and Deep Sea of Prydz Bay, Antarctica

A viral metagenomic analysis of five surface and two bottom water (878 meters below surface, mbs, and 3,357 mbs) samples from Prydz Bay, was conducted during February–March 2015. The results demonstrated that most of the DNA viruses were dsDNA viruses (79.73–94.06%, except at PBI1, 37.51%). Of these, Caudovirales (Siphoviridae, Myoviridae, and Podoviridae) phages were most abundant in surface seawater (67.67–71.99%), while nucleocytoplasmic large DNA viruses (NCLDVs) (Phycodnaviridae, Mimiviridae, and Pandoraviridae accounted for &gt;30% of dsDNA viruses) were most abundant in the bottom water (3,357 mbs). Of the ssDNA viruses, Microviridae was the dominant family in PBI2, PBI3, PBOs, and PBI4b (57.09–87.55%), while Inoviridae (58.16%) was the dominant family in PBI1. Cellulophaga phages (phi38:1 and phi10:1) and Flavobacterium phage 11b, infecting the possible host strains affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, were abundant in surface water dsDNA viromes. The long contig (PBI2_1_C) from the viral metagenomes were most similar to the genome architectures of Cellulophaga phage phi10:1 and Flavobacterium phage 11b from the Arctic Ocean. Comparative analysis showed that the surface viral community of Prydz Bay could be clearly separated from other marine and freshwater environments. The deep sea viral community was similar to the deep sea viral metagenome at A Long-term Oligotrophic Habitat Assessment Station (ALOHA, at 22°45′N, 158°00′W). The multivariable analysis indicated that nutrients probably played an important role in shaping the local viral community structure. This study revealed the preliminary characteristics of the viral community in Prydz Bay, from both the surface and the deep sea. It provided evidence of the relationships between the virome and the environment in Prydz Bay and provided the first data from the deep sea viral community of the Southern Ocean

Sequence variations in DNA repair gene XPC is associated with lung cancer risk in a Chinese population: a case-control study

<p>Abstract</p> <p>Background</p> <p>The nucleotide excision repair (NER) protein, xeroderma pigmentosum C (XPC), participates in recognizing DNA lesions and initiating DNA repair in response to DNA damage. Because mutations in <it>XPC </it>cause a high risk of cancer in XP patients, we hypothesized that inherited sequence variations in <it>XPC </it>may alter DNA repair and thus susceptibility to cancer.</p> <p>Methods</p> <p>In this hospital-based case-control study, we investigated five <it>XPC </it>tagging, common single nucleotide polymorphisms (tagging SNPs) in 1,010 patients with newly diagnosed lung cancer and 1,011 matched cancer free controls in a Chinese population.</p> <p>Results</p> <p>In individual tagging SNP analysis, we found that rs3731055<it>AG+AA </it>variant genotypes were associated with a significantly decreased risk of lung adenocarcinoma [adjusted odds ratio (OR), 0.71; 95% confidence interval (CI), 0.56–0.90] but an increased risk of small cell carcinomas [adjusted OR, 1.79; 95% CI, 1.05–3.07]. Furthermore, we found that haplotype <it>ACCCA </it>was associated with a decreased risk of lung adenocarcinoma [OR, 0.78; 95% CI, 0.62–0.97] but an increased risk of small cell carcinomas [OR, 1.68; 95% CI, 1.04–2.71], which reflected the presence of rs3731055<it>A </it>allele in this haplotype. Further stratified analysis revealed that the protective effect of rs3731055<it>AG+AA </it>on risk of lung adenocarcinoma was more evident among young subjects (age ≤ 60) and never smokers.</p> <p>Conclusion</p> <p>These results suggest that inherited sequence variations in <it>XPC </it>may modulate risk of lung cancer, especially lung adenocarcinoma, in Chinese populations. However, these findings need to be verified in larger confirmatory studies with more comprehensively selected tagging SNPs.</p

A Framework for Testing Scientific Software: A Case Study of Testing Amsterdam Discrete Dipole Approximation Software

Software testing with scientific software systems often suffers from test oracle problem, i.e., lack of test oracles. Amsterdam discrete dipole approximation code (ADDA) is a scientific software system that can be used to simulate light scattering of scatterers of various types. Testing of ADDA suffers from "test oracle problem". In this thesis work, I established a testing framework to test scientific software systems and evaluated this framework using ADDA as a case study. To test ADDA, I first used CMMIE code as the pseudo oracle to test ADDA in simulating light scattering of a homogeneous sphere scatterer. Comparable results were obtained between ADDA and CMMIE code. This validated ADDA for use with homogeneous sphere scatterers. Then I used experimental result obtained for light scattering of a homogeneous sphere to validate use of ADDA with sphere scatterers. ADDA produced light scattering simulation comparable to the experimentally measured result. This further validated the use of ADDA for simulating light scattering of sphere scatterers. Then I used metamorphic testing to generate test cases covering scatterers of various geometries, orientations, homogeneity or non-homogeneity. ADDA was tested under each of these test cases and all tests passed. The use of statistical analysis together with metamorphic testing is discussed as a future direction. In short, using ADDA as a case study, I established a testing framework, including use of pseudo oracles, experimental results and the metamorphic testing techniques to test scientific software systems that suffer from test oracle problems. Each of these techniques is necessary and contributes to the testing of the software under test

A Framework for Testing Scientific Software: A Case Study of Testing Amsterdam Discrete Dipole Approximation Software

"Software testing with scientific software systems often suffers from test oracle problem, i.e., lack of test oracles. Amsterdam discrete dipole approximation code (ADDA) is a scientific software system that can be used to simulate light scattering of scatterers of various types. Testing of ADDA suffers from ""test oracle problem"". In this thesis work, I established a testing framework to test scientific software systems and evaluated this framework using ADDA as a case study. To test ADDA, I first used CMMIE code as the pseudo oracle to test ADDA in simulating light scattering of a homogeneous sphere scatterer. Comparable results were obtained between ADDA and CMMIE code. This validated ADDA for use with homogeneous sphere scatterers. Then I used experimental result obtained for light scattering of a homogeneous sphere to validate use of ADDA with sphere scatterers. ADDA produced light scattering simulation comparable to the experimentally measured result. This further validated the use of ADDA for simulating light scattering of sphere scatterers. Then I used metamorphic testing to generate test cases covering scatterers of various geometries, orientations, homogeneity or non-homogeneity. ADDA was tested under each of these test cases and all tests passed. The use of statistical analysis together with metamorphic testing is discussed as a future direction. In short, using ADDA as a case study, I established a testing framework, including use of pseudo oracles, experimental results and the metamorphic testing techniques to test scientific software systems that suffer from test oracle problems. Each of these techniques is necessary and contributes to the testing of the software under test.

Different innate immunity and clearance of in macrophages from White Leghorn and Tibetan Chickens

Salmonella enterica serovar Gallinarum biovar Pullorum ( S. Pullorum ) is responsible for the systemic salmonellosis in different breeds of chickens. Macrophages, as host cells, play a key role in the innate immune response following infection with S. Pullorum . In this study, we first generated macrophages from two breeds of chicken (White Leghorn (WL) and Tibetan Chickens (TC)) peripheral blood monocytes in vitro. Then, we showed that the production of interleukin-1β (IL-1β), macrophage inflammatory protein-1β (MIP-1β) and interleukin-10 (IL-10) in lipopolysaccharide (LPS)-treated macrophages was significantly higher compared with the unstimulated cells in TC. LPS triggered only more expression of IL-10 in WL macrophages. Furthermore, macrophages from TC eliminated intracellular bacteria more efficiently than those from WL after S. Pullorum infection at a multiplicity of infection (MOI) 1. In addition, the variation between individuals and sex had the crucial effect on the immune response to LPS and S. Pullorum invasion