Co-immunization with DNA vaccines encoding yidR and IL-17 augments host immune response against Klebsiella pneumoniae infection in mouse model.

Klebsiella pneumoniae is an important gram-negative bacterium that causes severe respiratory and healthcare-associated infections. Although antibiotic therapy is applied to treat severe infections caused by K. pneumoniae, drug-resistant isolates pose a huge challenge to clinical practices owing to adverse reactions and the mismanagement of antibiotics. Several studies have attempted to develop vaccines against K. pneumoniae, but there are no licensed vaccines available for the control of K. pneumoniae infection. In the current study, we constructed a novel DNA vaccine, pVAX1-YidR, which encodes a highly conserved virulence factor YidR and a recombinant expression plasmid pVAX1-IL-17 encoding Interleukin-17 (IL-17) as a molecular adjuvant. Adaptive immune responses were assessed in immunized mice to compare the immunogenicity of the different vaccine schemes. The results showed that the targeted antigen gene was expressed in HEK293T cells using an immunofluorescence assay. Mice immunized with pVAX1-YidR elicited a high level of antibodies, induced strong cellular immune responses, and protected mice from K. pneumoniae challenge. Notably, co-immunization with pVAX1-YidR and pVAX1-IL-17 significantly augmented host adaptive immune responses and provided better protection against K. pneumoniae infections in vaccinated mice. Our study demonstrates that combined DNA vaccines and molecular adjuvants is a promising strategy to develop efficacious antibacterial vaccines against K. pneumoniae infections.

Characterization of a novel thermophilic cyanobacterium within Trichocoleusaceae, Trichothermofontia sichuanensis gen. et sp. nov., and its CO2-concentrating mechanism.

Thermophiles from extreme thermal environments have shown tremendous potential regarding ecological and biotechnological applications. Nevertheless, thermophilic cyanobacteria remain largely untapped and are rarely characterized. Herein, a polyphasic approach was used to characterize a thermophilic strain, PKUAC-SCTB231 (hereafter B231), isolated from a hot spring (pH 6.62, 55.5°C) in Zhonggu village, China. The analyses of 16S rRNA phylogeny, secondary structures of 16S-23S ITS and morphology strongly supported strain B231 as a novel genus within Trichocoleusaceae. Phylogenomic inference and three genome-based indices further verified the genus delineation. Based on the botanical code, the isolate is herein delineated as Trichothermofontia sichuanensis gen. et sp. nov., a genus closely related to a validly described genus Trichocoleus. In addition, our results suggest that Pinocchia currently classified to belong to the family Leptolyngbyaceae may require revision and assignment to the family Trichocoleusaceae. Furthermore, the complete genome of Trichothermofontia B231 facilitated the elucidation of the genetic basis regarding genes related to its carbon-concentrating mechanism (CCM). The strain belongs to ß-cyanobacteria according to its ß-carboxysome shell protein and 1B form of Ribulose bisphosphate Carboxylase-Oxygenase (RubisCO). Compared to other thermophilic strains, strain B231contains a relatively low diversity of bicarbonate transporters (only BicA for HCO3- transport) but a higher abundance of different types of carbonic anhydrase (CA), ß-CA (ccaA) and γ-CA (ccmM). The BCT1 transporter consistently possessed by freshwater cyanobacteria was absent in strain B231. Similar situation was occasionally observed in freshwater thermal Thermoleptolyngbya and Thermosynechococcus strains. Moreover, strain B231 shows a similar composition of carboxysome shell proteins (ccmK1-4, ccmL, -M, -N, -O, and -P) to mesophilic cyanobacteria, the diversity of which was higher than many thermophilic strains lacking at least one of the four ccmK genes. The genomic distribution of CCM-related genes suggests that the expression of some components is regulated as an operon and others in an independently controlled satellite locus. The current study also offers fundamental information for future taxogenomics, ecogenomics and geogenomic studies on distribution and significance of thermophilic cyanobacteria in the global ecosystem.

Characterization of Molecular Diversity and Organization of Phycobilisomes in Thermophilic Cyanobacteria.

Thermophilic cyanobacteria are cosmopolitan and abundant in the thermal environment. Their light-harvesting complexes, phycobilisomes (PBS), are highly important in photosynthesis. To date, there is limited information on the PBS composition of thermophilic cyanobacteria whose habitats are challenging for survival. Herein, genome-based methods were used to investigate the molecular components of PBS in 19 well-described thermophilic cyanobacteria. These cyanobacteria are from the genera Leptolyngbya, Leptothermofonsia, Ocullathermofonsia, Thermoleptolyngbya, Trichothermofonsia, Synechococcus, Thermostichus, and Thermosynechococcus. According to the phycobiliprotein (PBP) composition of the rods, two pigment types are observed in these thermophiles. The amino acid sequence analysis of different PBP subunits suggests several highly conserved cysteine residues in these thermophiles. Certain amino acid contents in the PBP of thermophiles are significantly higher than their mesophilic counterparts, highlighting the potential roles of specific substitutions of amino acid in the adaptive thermostability of light-harvesting complexes in thermophilic cyanobacteria. Genes encoding PBS linker polypeptides vary among the thermophiles. Intriguingly, motifs in linker apcE indicate a photoacclimation of a far-red light by Leptolyngbya JSC-1, Leptothermofonsia E412, and Ocullathermofonsia A174. The composition pattern of phycobilin lyases is consistent among the thermophiles, except for Thermostichus strains that have extra homologs of cpcE, cpcF, and cpcT. In addition, phylogenetic analyses of genes coding for PBPs, linkers, and lyases suggest extensive genetic diversity among these thermophiles, which is further discussed with the domain analyses. Moreover, comparative genomic analysis suggests different genomic distributions of PBS-related genes among the thermophiles, indicating probably various regulations of expression. In summary, the comparative analysis elucidates distinct molecular components and organization of PBS in thermophilic cyanobacteria. These results provide insights into the PBS components of thermophilic cyanobacteria and fundamental knowledge for future research regarding structures, functions, and photosynthetic improvement.

Dockey: a modern integrated tool for large-scale molecular docking and virtual screening.

Molecular docking is a structure-based and computer-aided drug design approach that plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most widely used molecular docking tool for study of protein-ligand interactions and virtual screening. Although many tools have been developed to streamline and automate the AutoDock docking pipeline, some of them still use outdated graphical user interfaces and have not been updated for a long time. Meanwhile, some of them lack cross-platform compatibility and evaluation metrics for screening lead compound candidates. To overcome these limitations, we have developed Dockey, a flexible and intuitive graphical interface tool with seamless integration of several useful tools, which implements a complete docking pipeline covering molecular sanitization, molecular preparation, paralleled docking execution, interaction detection and conformation visualization. Specifically, Dockey can detect the non-covalent interactions between small molecules and proteins and perform cross-docking between multiple receptors and ligands. It has the capacity to automatically dock thousands of ligands to multiple receptors and analyze the corresponding docking results in parallel. All the generated data will be kept in a project file that can be shared between any systems and computers with the pre-installation of Dockey. We anticipate that these unique characteristics will make it attractive for researchers to conduct large-scale molecular docking without complicated operations, particularly for beginners. Dockey is implemented in Python and freely available at https://github.com/lmdu/dockey.

Repurposing Dimetridazole and Ribavirin to disarm Pseudomonas aeruginosa virulence by targeting the quorum sensing system.

Pseudomonas aeruginosa relies on its complex cellular regulatory network to produce a series of virulence factors and to cause various acute and chronic infections in a wide range of hosts. Compared with traditional antibiotics which frequently accompany with widespread antibiotic resistance, crippling the virulence system of bacteria is expected to be a promising anti-infective strategy. In this study, Dimetridazole and Ribavirin, which had poor antibacterial activities on P. aeruginosa reference isolate PAO1 in nutrient medium but significantly inhibited the growth of P. aeruginosa PAO1 in M9-adenosine, were selected from 40 marketed compounds with similar core structure (furan, benzofuran, or flavonoids) to the acyl-homoserine lactone signals of P. aeruginosa quorum sensing (QS) system. The production of QS-controlled proteases, pyocyanin, and biofilm formation of P. aeruginosa PAO1 and the clinical isolates were significantly decreased by the presence of Dimetridazole or Ribavirin. Correspondingly, the majority of QS-activated genes in P. aeruginosa, including the key regulatory genes lasR, rhlR, and pqsR and their downstream genes, were significantly inhibited by Ribavirin or Dimetridazole, as determined by RNA-sequencing and quantitative PCR. Furthermore, the susceptibilities of drug-resistant P. aeruginosa isolates to polymyxin B, meropenem, and kanamycin were remarkably promoted by the synergistic application of Dimetridazole or Ribavirin. Finally, the treatment of Ribavirin or Dimetridazole effectively protected Caenorhabditis elegans and mice from P. aeruginosa infection. In conclusion, this study reports the antivirulence potentials of Dimetridazole and Ribavirin on P. aeruginosa and provides structural basis and methodological reference for the development of anti-pseudomonal drugs.

Reevaluation of Parasynechococcus-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites.

Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)n, (AG)n and (AGC)n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments.

Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae.

Thermal environments are an important reservoir of thermophiles with significant ecological and biotechnological potentials. However, thermophilic isolates remain largely unrecovered from their habitats and are rarely systematically identified. In this study, we characterized using polyphasic approaches a thermophilic strain, PKUAC-SCTAE412 (E412 hereafter), recovered from Lotus Lake hot spring based in Ganzi prefecture, China. The results of 16S rRNA/16S-23S ITS phylogenies, secondary structure, and morphology comparison strongly supported that strain E412 represent a novel genus within Leptolyngbyaceae. This delineation was further confirmed by genome-based analyses [phylogenomic inference, average nucleotide/amino-acid identity, and the percentages of conserved proteins (POCP)]. Based on the botanical code, the isolate is herein delineated as Leptothermofonsia sichuanensis gen. sp. nov, a genus adjacent to recently delineated Kovacikia and Stenomitos. In addition, we successfully obtained the first complete genome of this new genus. Genomic analysis revealed its adaptations to the adverse hot spring environment and extensive molecular components related to mobile genetic elements, photosynthesis, and nitrogen metabolism. Moreover, the strain was capable of modifying the composition of its light-harvesting apparatus depending on the wavelength and photoperiod, showing chromatic adaptation capacity characteristic for T1 and T2 pigmentation types. Other physiological studies showed the strain's ability to utilize sodium bicarbonate and various sulfur compounds. The strain was also shown to be diazotrophic. Interestingly, 24.6% of annotated protein-coding genes in the E412 genome were identified as putatively acquired, hypothesizing that a large number of genes acquired through HGT might contribute to the genome expansion and habitat adaptation of those thermophilic strains. Most the HGT candidates (69.4%) were categorized as metabolic functions as suggested by the KEGG analysis. Overall, the complete genome of strain E412 provides the first insight into the genomic feature of the genus Leptothermofonsia and lays the foundation for future global ecogenomic and geogenomic studies.

Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria.

Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of Leptolyngbya-like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size (p < 0.01) and negatively correlated with GC content (p < 0.05). Moreover, the motif (A/C)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of Leptolyngbya-like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of Leptolyngbya strains to globally diverse niches.

Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China.

Thermoleptolyngbya is a newly proposed genus of thermophilic cyanobacteria that are often abundant in thermal environments. However, a vast majority of Thermoleptolyngbya strains were not systematically identified, and genomic features of this genus are also sparse. Here, polyphasic approaches were employed to identify a thermophilic strain, PKUAC-SCTA183 (A183 hereafter), isolated from hot spring Erdaoqiao, Ganzi prefecture, China. Whole-genome sequencing of the strain revealed its allocation to Thermoleptolyngbya sp. and genetic adaptations to the hot spring environment. While the results of 16S rRNA were deemed inconclusive, the more comprehensive polyphasic approach encompassing phenetic, chemotaxic, and genomic approaches strongly suggest that a new taxon, Thermoleptolyngbya sichuanensis sp. nov., should be delineated around the A183 strain. The genome-scale phylogeny and average nucleotide/amino-acid identity confirmed the genetic divergence of the A183 strain from other strains of Thermoleptolyngbya along with traditional methods such as 16S-23S ITS and its secondary structure analyses. Comparative genomic and phylogenomic analyses revealed inconsistent genome structures between Thermoleptolyngbya A183 and O-77 strains. Further gene ontology analysis showed that the unique genes of the two strains were distributed in a wide range of functional categories. In addition, analysis of genes related to thermotolerance, signal transduction, and carbon/nitrogen/sulfur assimilation revealed the ability of this strain to adapt to inhospitable niches in hot springs, and these findings were preliminarily confirmed using experimental, cultivation-based approaches.

Antibiotic intervention redisposes bacterial interspecific interacting dynamics in competitive environments.

Interspecific interaction happens frequently among bacterial species and can promote the colonization of polymicrobial community in various environments. However, it is not clear whether the intervention of antibiotics, which is a common therapeutic method for infectious disease, will influence the interacting dynamics of different pathogenic bacteria. By using the frequently co-isolated bacteria Pseudomonas aeruginosa and Staphylococcus aureus as models, here we identify an antibiotic-determined mutual invasion relationship between bacterial pathogens. We show that although P. aeruginosa has a significant intrinsic competitive advantage over S. aureus by producing the quorum-sensing (QS)-controlled anti-staphylococcal molecules, methicillin-resistant S. aureus (MRSA) can inhibit neighbouring P. aeruginosa in the presence of subinhibitory aminoglycoside antibiotics (e.g. streptomycin) to P. aeruginosa. Importantly, subinhibitory streptomycin decreases the expression of QS-regulated genes in P. aeruginosa and thus relieves the survival stress of MRSA brought by P. aeruginosa. On the other side, the iron-uptake systems and pathogenicity of MRSA can be enhanced by the extracellular products of streptomycin-treated P. aeruginosa. Therefore, this study provides an explanation for the substitution of dominant species and persistent coexistence of bacterial pathogens in the host with repeated antibiotic therapies and contributes to further understanding the pathogenesis of chronic polymicrobial infections.

Characterization of a Novel Hot-Spring Cyanobacterium Leptodesmis sichuanensis sp. Nov. and Genomic Insights of Molecular Adaptations Into Its Habitat.

The newly described genus Leptodesmis comprises several strains of filamentous cyanobacteria from diverse, primarily cold, habitats. Here, we sequenced the complete genome of a novel hot-spring strain, Leptodesmis sp. PKUAC-SCTA121 (hereafter A121), isolated from Erdaoqiao hot springs (pH 6.32, 40.8°C), China. The analyses of 16S rRNA/16S-23S ITS phylogenies, secondary structures, and morphology strongly support strain A121 as a new species within Leptodesmis, Leptodesmis sichuanensis sp. nov. Notably, strain A121 is the first thermophilic representative of genus Leptodesmis and more broadly the first Leptodesmis sp. to have its genome sequenced. In addition, results of genome-scale phylogenetic analysis and average nucleotide/amino acid identity as well as in silico DNA-DNA hybridization and patristic analysis verify the establishment of genus Leptodesmis previously cryptic to Phormidesmis. Comparative genomic analyses reveal that the Leptodesmis A121 and Thermoleptolyngbya sichuanensis A183 from the same hot-spring biome exhibit different genome structures but similar functional classifications of protein-coding genes. Although the core molecular components of photosynthesis, metabolism, and signal transduction were shared by the two strains, distinct genes associated with photosynthesis and signal transduction were identified, indicating that different strategies might be used by these strains to adapt to that specific niche. Furthermore, the complete genome of strain A121 provides the first insight into the genomic features of genus Leptodesmis and lays the foundation for future global ecogenomic and geogenomic studies.

Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files.

FASTA and FASTQ are the most widely used biological data formats that have become the de facto standard to exchange sequence data between bioinformatics tools. With the avalanche of next-generation sequencing data, the amount of sequence data being deposited and accessed in FASTA/Q formats is increasing dramatically. However, the existing tools have very low efficiency at random retrieval of subsequences due to the requirement of loading the entire index into memory. In addition, most existing tools have no capability to build index for large FASTA/Q files because of the limited memory. Furthermore, the tools do not provide support to randomly accessing sequences from FASTA/Q files compressed by gzip, which is extensively adopted by most public databases to compress data for saving storage. In this study, we developed pyfastx as a versatile Python package with commonly used command-line tools to overcome the above limitations. Compared to other tools, pyfastx yielded the highest performance in terms of building index and random access to sequences, particularly when dealing with large FASTA/Q files with hundreds of millions of sequences. A key advantage of pyfastx over other tools is that it offers an efficient way to randomly extract subsequences directly from gzip compressed FASTA/Q files without needing to uncompress beforehand. Pyfastx can easily be installed from PyPI (https://pypi.org/project/pyfastx) and the source code is freely available at https://github.com/lmdu/pyfastx.

Genetic and Functional Diversity of Pseudomonas aeruginosa in Patients With Chronic Obstructive Pulmonary Disease.

Pseudomonas aeruginosa is the most relevant pathogen to the severe exacerbations of patients with chronic obstructive pulmonary disease (COPD). However, the genetic and functional characteristics of P. aeruginosa isolates from COPD airways still remain less understood. In this study, the genetic, phylogenetic, phenotypic, and transcriptional features of P. aeruginosa isolates from COPD sputa were comprehensively explored by susceptibility testing, comparative-genomic analysis, phylogenetic analysis, phenotypic profiling, and comparative-transcriptomic analysis. We found that P. aeruginosa was prevalent in elder COPD patients and highly resisted to many commonly used antibiotics. P. aeruginosa COPD isolates harbored a substantial number of variant sites that might influence the primary metabolism and substance transport system. These isolates were discretely distributed in the phylogenetic tree and clustered with internationally collected P. aeruginosa in two major groups, and could be classified into three groups according to their differences in virulence-related phenotypes. Furthermore, the transcriptional patterns of COPD isolates could be classified into PAO1-like group with reduced protein secretion and motility and PAO1-distinct group with decreased substance transport but enhanced primary metabolism. In conclusion, this study demonstrates that P. aeruginosa isolates from COPD patients have abundant genetic and phenotypic diversity, and provides an important reference for further exploring the survival strategy of P. aeruginosa in COPD airways and the development of anti-pseudomonal therapy.

MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques.

Macaques are the most widely used non-human primates in biomedical research. The genetic divergence between these animal models is responsible for their phenotypic differences in response to certain diseases. However, the macaque single nucleotide polymorphism resources mainly focused on rhesus macaque (Macaca mulatta), which hinders the broad research and biomedical application of other macaques. In order to overcome these limitations, we constructed a database named MACSNVdb that focuses on the interspecies genetic diversity among macaque genomes. MACSNVdb is a web-enabled database comprising ~74.51 million high-quality non-redundant single nucleotide variants (SNVs) identified among 20 macaque individuals from six species groups (muttla, fascicularis, sinica, arctoides, silenus, sylvanus). In addition to individual SNVs, MACSNVdb also allows users to browse and retrieve groups of user-defined SNVs. In particular, users can retrieve non-synonymous SNVs that may have deleterious effects on protein structure or function within macaque orthologs of human disease and drug-target genes. Besides position, alleles and flanking sequences, MACSNVdb integrated additional genomic information including SNV annotations and gene functional annotations. MACSNVdb will facilitate biomedical researchers to discover molecular mechanisms of diverse responses to diseases as well as primatologist to perform population genetic studies. We will continue updating MACSNVdb with newly available sequencing data and annotation to keep the resource up to date. Database URL: http://big.cdu.edu.cn/macsnvdb/.

PSMD: An extensive database for pan-species microsatellite investigation and marker development.

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan-Species Microsatellite Database, http://big.cdu.edu.cn/psmd/) as a web-based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome-wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user-defined parameters. Furthermore, Primer3 was embedded to help users to design high-quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.

A systematic genotype and subgenotype re-ranking of hepatitis B virus under a novel classification standard.

BACKGROUND AND AIM: It is commonly noticed that chaotic and inefficient subgenotyping are universally used academically and clinically, a standardized HBV genotype/subgenotype classification criterion is urgently acquired. Sequence similarity, which was commonly used for the last three decades, should be upgraded by phylogenetic analysis in genotyping of recombinant-free HBV strains. METHODS: In this study, 4,429 HBV whole-genome sequences were employed to reconstruct the phylogeny of HBV using Bayesian inference. After excluding recombinant sequences, calculating partitioned evolutionary models, excluding recombinant sequences, reconstructing phylogenetic trees, and performing a correlation analysis of genetic distances, geographical distribution and serotypes, we systematically redefined the genotypes and subgenotypes of HBV. RESULTS: Compared to previous taxonomy, fourteen subgenotypes (A5-A7; B5-B9; C2-C4, C7; and D6-D7) were revised in the new standard. Now the HBV is divided into ten genotypes (A-J) and 24 subgenotypes (A1-A3; B1-B5; C1-C6; D1-D6; and F1-F4). CONCLUSION: Our robust genotype/subgenotype new taxonomy has objectively re-molded the current shape of HBV classification. We believe that all future hepatitis B related researches or diagnosis will be benefited under the new HBV genotyping/subgenotyping standards.

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations.

BACKGROUND: Microbial communities are susceptible to the public goods dilemma, whereby individuals can gain an advantage within a group by utilizing, but not sharing the cost of producing, public goods. In bacteria, the development of quorum sensing (QS) can establish a cooperation system in a population by coordinating the production of costly and sharable extracellular products (public goods). Cooperators with intact QS system and robust ability in producing public goods are vulnerable to being undermined by QS-deficient defectors that escape from QS but benefit from the cooperation of others. Although microorganisms have evolved several mechanisms to resist cheating invasion in the public goods game, it is not clear why cooperators frequently coexist with defectors and how they form a relatively stable equilibrium during evolution. RESULTS: We show that in Pseudomonas aeruginosa, QS-directed social cooperation can select a conditional defection strategy prior to the emergence of QS-mutant defectors, depending on resource availability. Conditional defectors represent a QS-inactive state of wild type (cooperator) individual and can invade QS-activated cooperators by adopting a cheating strategy, and then revert to cooperating when there are abundant nutrient supplies irrespective of the exploitation of QS-mutant defector. Our mathematical modeling further demonstrates that the incorporation of conditional defection strategy into the framework of iterated public goods game with sound punishment mechanism can lead to the coexistence of cooperator, conditional defector, and defector in a rock-paper-scissors dynamics. CONCLUSIONS: These findings highlight the importance of behavioral heterogeneity in stabilizing the population structure and provide a potential reasonable explanation for the maintenance and evolution of cooperation in microbial communities.

Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat.

Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.

Transcriptome analysis reveals immune-related gene expression changes with age in giant panda (Ailuropoda melanoleuca) blood.

The giant panda (Ailuropoda melanoleuca), an endangered species endemic to western China, has long been threatened with extinction that is exacerbated by highly contagious and fatal diseases. Aging is the most well-defined risk factor for diseases and is associated with a decline in immune function leading to increased susceptibility to infection and reduced response to vaccination. Therefore, this study aimed to determine which genes and pathways show differential expression with age in blood tissues. We obtained 210 differentially expressed genes by RNA-seq, including 146 up-regulated and 64 down-regulated genes in old pandas (18-21yrs) compared to young pandas (2-6yrs). We identified ISG15, STAT1, IRF7 and DDX58 as the hub genes in the protein-protein interaction network. All of these genes were up-regulated with age and played important roles in response to pathogen invasion. Functional enrichment analysis indicated that up-regulated genes were mainly involved in innate immune response, while the down-regulated genes were mainly related to B cell activation. These may suggest that the innate immunity is relatively well preserved to compensate for the decline in the adaptive immune function. In conclusion, our findings will provide a foundation for future studies on the molecular mechanisms underlying immune changes associated with ageing.

The first draft genome of Lophophorus: A step forward for Phasianidae genomic diversity and conservation.

The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100.93 Mb (9.97%) repeat elements, 785 ncRNA, 5,465,549 bp (0.54%) SSR and 15,550 (92%) genes in public databases. Compared to other birds and mammals, the genome evolution analysis showed numerous expanded gene families and positive selected genes involved in high-altitude adaptation, especially related to the adaptation of low temperature and hypoxia. Consequently, this gene data can be used to investigate the molecular evolution of high-altitude adaptation in future bird research. Our first published genome of the genus Lophophorus will be integral for the study of monal population genetic diversity and conservation, genomic evolution and Galliformes species differentiation in the Qinghai-Tibetan Plateau.