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ABSTRACTH6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.

Abstract Background Genomic three-dimensional (3D) spatial organization plays a key role in shaping gene expression and associated chromatin modification, and it is highly sensitive to environmental stress conditions. In microalgae, exposure to nitrogen stress can drive lipid accumulation, yet the associated functional alterations in the spatial organization of the microalgal genome have yet to be effectively characterized. Results Accordingly, the present study employed RNA-seq, Hi-C, and ChIP-seq approaches to explore the relationship between 3D chromosomal architecture and gene expression during lipid accumulation in the marine microalga Nannochloropsis oceanica in response to nitrogen deprivation (ND). These analyses revealed that ND resulted in various changes in chromosomal organization, including A/B compartment transitions, topologically associating domain (TAD) shifts, and the disruption of short-range interactions. Significantly higher levels of gene expression were evident in A compartments and TAD boundary regions relative to B compartments and TAD interior regions, consistent with observed histone modification enrichment in these areas. ND-induced differentially expressed genes (DEGs) were notably enriched in altered TAD-associated regions and regions exhibiting differential genomic contact. These DEGs were subjected to Gene Ontology (GO) term analyses that indicated they were enriched in the ‘fatty acid metabolism’, ‘response to stress’, ‘carbon fixation’ and ‘photosynthesis’ functional categories, in line with the ND treatment conditions used to conduct this study. These data indicate that Nannochloropsis cells exhibit a clear association between chromatin organization and transcriptional activity under nitrogen stress conditions. Pronounced and extensive histone modifications were evident in response to ND. Observed changes in chromatin architecture were linked to shifts in histone modifications and gene expression. Conclusions Overall, the reprogramming of many lipid metabolism-associated genes was evident under nitrogen stress conditions with respect to both histone modifications and chromosomal organization. Together these results revealed that higher-order chromatin architecture represents a new layer that can guide efforts to understand the transcriptional regulation of lipid metabolism in nitrogen-deprived microalgae.

Ceriops tagal is an inner mangrove tree species and well known medicinal plant with wide distribution in the world mangal. Here, we reported and characterized its complete chloroplast genome sequence assembled from short reads generated by Illumina sequencing. Total chloroplast genome size was164,439 bp, including inverted repeats (IRs) of 26,390 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 92,489 bp and 20,172bp, respectively. A total of 134 genes, including 42 tRNA, 8 rRNA, and 84 protein-coding genes, were identified. Among them, 17 genes occur in IRs, containing six protein-coding genes, four rRNA genes and seven tRNA genes. The GC content of C. tagal is 35.32%. Phylogenetic analysis using the maximum likelihood algorithm showed that C. tagal is sister to a clade with three species in the order Rosales.

Normalized difference vegetation index (NDVI) derived from satellites has been ubiquitously utilized in the field of remote sensing. Nevertheless, there are multitudinous contaminations in NDVI time series because of the atmospheric disturbance, cloud cover, sensor failure, and so on. It is crucial to remove the noises prior to further applications. Numerous techniques have been proposed to alleviate this issue in the last few decades. To the best of our knowledge, there hasn’t been a systematical study to summarize and analyze the status of NDVI time series reconstruction techniques since 1980s. As a result, our goal is to recapitulate the current approaches for reconstructing high-quality NDVI time series, followed by an interpretation on the principle, merits and demerits of different kinds of methods. They were mainly classified into temporal-based methods, frequency-based methods and hybrid methods. The evaluation approaches on the quality of NDVI reconstruction were introduced, accompanied with the future development tendency.

The Tibetan Plateau (TP) is an important component of the global environmental system, on which the snow cover greatly affects the regional climate and ecology. Moderate resolution imaging spectroradiometer (MODIS) snow cover products have been demonstrated to be appropriate for investigating the snow cover over the TP. However, they are subject to cloud obscuration, and the TP’s extremely complex terrain makes the snow monitoring difficult. Therefore, in this paper, we propose a two-stage spatio−temporal fusion framework for the cloud removal of MODIS C6 snow products, including an adjusted Terra and Aqua combination (TAC) and a spatio−temporal fusion based on Gaussian kernel function and error correction (STF-GKF-EC). To the best of our knowledge, this is the first time that a spatio−temporally continuous daily 500-m MODIS normalized difference snow index (NDSI) product has been generated for the TP, which greatly improves the spatial and temporal resolutions of the current snow cover products. The main stage, STF-GKF-EC, adaptively weights the spatial and temporal correlations by the Gaussian kernel function, and further takes the rapid changes of snow cover into consideration through the error correction. The experiments indicated that STF-GKF-EC removes clouds completely, achieving an overall accuracy (OA) and mean absolute error (MAE) of 91.48% and 3.88, respectively. Based on the cloud-removed results, during 2001−2017, as far as the intra-annual variation is concerned, a large proportion of the snow cover appears between October and May, with a peak in February/March, and the variation is mainly controlled by temperature. For the inter-annual variation, an obvious increasing trend of 0.68/year for NDSI is observed before 2005, followed by a slight decreasing trend of 0.16/year, in which precipitation is a better explanation factor than temperature.

Streptococcus agalactiae is one of the important causative agents of bovine mastitis. Studies on molecular epidemiology, virulence factors and antimicrobial susceptibility profiles of S. agalactiae isolates from mastitis in China are scarce. Thus, this study was carried out to investigate prevalence of S. agalactiae associated with subclinical mastitis, to determine antimicrobial susceptibility profile, and to analyze their phenotypic and genotypic profiles. Capsular serotypes and genotypes by multilocus serotyping and virulence genes (hemolysin III, C-β protein, C-α protein, surface protein rib, hyaluronate lyase, and C5a peptidase) were determined using molecular assays. Additionally, susceptibility of S. agalactiae isolates to antimicrobial agents was accessed through standard disc diffusion method. A total of 2225 milk samples were collected from 21 large dairy herds located in 10 provinces of China. Overall, 133 (14.1%) S. agalactiae isolates were recovered from 946 (42.5%) subclinical mastitis milk samples. Serotype Ia and ST103 were the most prevalent serotypes and genotypes. Five of the six virulence genes were detected in 22.6% isolates with only two virulence genes and 6.8% of isolates with three genes. There were no significant geographical differences in the distribution of virulence genes. Moreover, 63.9% of S. agalactiae exhibited resistance to levofloxacin, 3.8% isolates were resistant to cefepime, 2.3% were resistant to chloramphenicol and ampicillin. Additionally, two ampicillin/cefotaxime/ levofloxacin-resistant isolates, one vancomycin-resistant isolate and one ampicillin/cefotaxime-resistant isolate were identified. This study concludes high prevalence of S. agalactiae from subclinical mastitis carrying virulence genes and mainly belonging to Serotype Ia and ST103. [ABSTRACT FROM AUTHOR]

Bacillus amyloliquefaciens is one of most prevalent Gram-positive aerobic spore-forming bacteria with the ability to synthesize polysaccharides and polypeptides. Here, we report the complete genome sequence of B. amyloliquefaciens LL3, which was isolated from fermented food and presents the glutamic acid-independent production of poly-γ-glutamic acid [ABSTRACT FROM AUTHOR]