Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge.

A novel pale white-pigmented bacterial strain designated YC-7-48T was isolated from activated sludge in China. Cells of the strain, which grew at 15-37 °C (optimum at 30 °C) and pH 6.0-9.0 (optimum at 7.0), were Gram-stain-negative, rod-shaped and motile. Strain YC-7-48T had 97.4-97.1% 16S rRNA gene sequence similarity to type strains of eight species in the genera Pusillimonas, Eoetvoesia, Paralcaligenes, Parapusillimonas and Paracandidimonas of the family Alcaligenaceae. Phylogenetic analysis based on 16S rRNA gene sequencing placed the strain on a separate branch in the genus Pusillimonas and showed that it exhibited 97.4, 97.3 and 96.6% similarity to Pusillimonas caeni EBR-8-1T, Pusillimonas noertemannii BN9T and Pusillimonas maritima 17-4AT, respectively. The genome size of strain YC-7-48T was 3202438 bp, with 54.3 mol% G+C content. According to the genome analysis, YC-7-48T encodes several heavy metal resistance proteins and enzymes related to the metabolism of nicotine and aromatic compounds. The results of digital DNA-DNA hybridization and average nucleotide identity analyses based on whole genome sequences between strain YC-7-48T and the closely related strains indicated that the strain represented a new species of the genus Pusillimonas. The chemotaxonomic results identified Q-8 as the predominant respiratory quinone, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and two unidentified aminolipids as the major polar lipids, and C16:0 (27.4 %), C17:0 cyclo (22.0 %), C18:0 (11.7 %) and C19:0 cyclo ω8c (9.5 %) as the major fatty acids. Thus, based on morphological, chemotaxonomic and phylogenetic characterization and genomic data, we proposed that the isolate is a representative of a novel species named Pusillimonas minor sp. nov., with the type strain YC-7-48T (=CGMCC 1.17466T=KACC 21349T).

A non-mammalian Toll-like receptor 26 (TLR26)gene mediates innate immune responses in yellow catfish Pelteobagrus fulvidraco.

In this study, we identified a fish-specific Toll-like receptor (TLR) in Pelteobagrus fulvidraco, an economically important freshwater fish in China. This TLR, PfTLR26, was shown to be encoded by a 3084 bp open reading frame (ORF), producing a polypeptide 1027 amino acids in length. The PfTLR26 protein contains a signal peptide, eight leucine-rich repeat (LRR) domains, two LRR_TYP domains in the extracellular region, and a Toll/interleukin (IL)-1 receptor (TIR) domain in the cytoplasmic region, consistent with the characteristic TLR domain architecture. This predicted 117.1 kDa protein was highly homologous to those of other fish, with phylogenetic analysis revealing the closest relation to TLR26 of Ictalurus punctatus. Real-time quantitative reverse transcription-PCR (qRT-PCR) analysis showed that the PfTLR26 gene was expressed in all tissues tested, with the highest expression levels seen in the head kidney and blood, and the lowest seen in muscle. PfTLR26 exhibited significant upregulation in liver, spleen, head kidney, and blood at different time points following challenge with the common TLR agonists lipopolysaccharide (LPS) and polyriboinosinic polyribocytidylic acid (Poly I:C). Taken together, these results suggest that PfTLR26 may be an important component of the P. fulvidraco innate immune system, participating in the transduction of TLR signaling under pathogen stimulation.

Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge.

To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.

New insight into the molecular basis of Fe (III) stress responses of Procambarus clarkii by transcriptome analysis.

Iron in excess can have toxic effects on living organisms. In China, the freshwater crayfish Procambarus clarkii is a source of aquatic food with high-quality protein and has significant commercial value. P. clarkii shows oxidative stress on exposure to heavy metals, and antioxidant enzymes, such as ubiquitination enzymes and proteasomes, play important roles in oxidative stress. To understand the antioxidant defense system of P. clarkii, we analyzed the hepatopancreas transcriptomes of P. clarkii after stimulation with FeCl3. In total, 5199 differentially expressed genes (DEGs) were identified (2747 upregulated and 2452 downregulated). GO analysis revealed that these DEGs belonged to 16 cellular component, 16 molecular function, and 19 biological process subcategories. A total of 1069 DEGs were classified into 25 categories by using COG. Some antioxidant defense pathways, such as "Ubiquitin mediated proteolysis" and "Glutathione metabolism," were identified using KEGG. In addition, quantitative real time-PCR (qRT-PCR) substantiated the up-regulation of a random selection of DEGs including antioxidant and immune defense genes. We obtained information for P. clarkii transcriptome databases and new insights into the responses of P. clarkii hepatopancreas to heavy metals.

Comparative mitochondrial genome analysis of Grammodes geometrica and other noctuid insects reveals conserved mitochondrial genome organization and phylogeny.

The mitochondrial genome (mitogenome) plays an important role in revealing molecular evolution. In this study, the complete mitogenome of Grammodes geometrica (G. geometrica) (Lepidoptera: Erebidae) was sequenced and characterized. The nucleotide composition of the genome is highly A + T biased, accounting for 80.49%. Most protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome oxidase subunit 1 (cox1) gene, which was initiated by CGA. The order and orientation of genes with the order trnM-trnI-trnQ-nad2 is a typical rearrangement compared with those ancestral insects in which trnM is located between trnQ and nad2. Most tRNA genes were folded into the typical cloverleaf structure except for trnS1 (AGN). The A + T-rich region contains the conserved motif "ATAGA" followed by a 19 bp poly-T stretch, which was also observed in other Noctuoidea species. In addition, we reconstructed phylogenetic trees among the nucleotide alignments of five families of Noctuoidea species except the Oenosandridae. Finally, we achieved a well-supported tree, which showed that G. geometrica belongs to the Erebidae family. Moreover, the relationships at the family-level can be displayed as follows: (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).

Transcriptome analysis of differential expressed genes in hepatopancreas of Procambarus clarkii challenged with peptidoglycan.

Procambarus clarkii is one of the most economically important species in Chinese aquaculture, and is widely cultured. Infection of P. clarkii populations with bacterial pathogens causes high mortality and great economic loss, therefore disease control is of significant economic importance. P. clarkii is a model system for studying immune responses in invertebrates, and its immune system consists solely of the innate response. In the present study, we examined gene expression related to immune function in P. clarkii in response to pathogen challenge. The transcriptome of hepatopancreas tissue from P. clarkii challenged with peptidoclycan (PGN) was analyzed and compared to control specimens. After assembly and annotation, 48,661 unigenes were identified with an average length of 671.54 bp. A total of 2533 differentially expressed genes (DEGs) were obtained, including 765 significantly up-regulated unigenes and 1757 significantly down-regulated unigenes. Gene ontology (GO) analysis demonstrated 19 biological process subcategories, 16 cellular component subcategories, and 17 molecular function subcategories that were enriched among these DEGs. Enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed enrichment among immune responses pathways. Taken together, this study not only enriches the existing P. clarkii transcriptome database, but also elucidates immune responses of crayfish that are activated in response to PGN challenge.

Transcriptome-wide identification of differentially expressed genes in Procambarus clarkii in response to chromium challenge.

Because of the high protein content and rich meat quality of crayfish Procambarus clarkii, it has become widely popular in China in recent years and has a high economic value. When P. clarkii is stimulated by heavy metals, it reacts to oxidation. P. clarkii has evolved antioxidant defense systems, including antioxidant enzymes such as catalase (CAT). The hexavalent form of Cr (VI) is a pathogenic factor that is of particular concern in aqueous systems because of its great toxicity to living organisms. In this study, we characterized the transcriptome of P. clarkii using a RNA sequencing method and performed a comparison between K2Cr2O7-treated samples and controls. In total, 34,237 unigenes were annotated. We identified 5098 significantly differentially expressed genes (DEGs), including 2536 and 2562 were significantly up-regulated and down-regulated, respectively. In addition, quantitative real time-PCR (qRT-PCR) confirmed the up-regulation of a random selection of DEGs. Our results contribute to a more comprehensive understanding of the antioxidant defense system used by P. clarkii in response to heavy metal stress.

The complete mitochondrial genome of Clostera anastomosis (Lepidoptera: Notodontidae) and implication for the phylogenetic relationships of Noctuoidea species.

In the present study, the complete mitochondrial genome (mitogenome) of Clostera anastomosis (C. anastomosis) has been determined for the first time. The mitogenome is 15,390 base pairs (bp) in length, comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and one non-coding control region (CR). The gene order shows a typical trnM rearrangement (trnM-trnI-trnQ) compared to ancestral insects (trnI-trnQ-trnM). Almost all the PCGs have the same start codon (ATN) except for cox1 (CGA), and almost all tRNAs have a typical cloverleaf secondary structure except for trnS1. At the beginning of the CR, we found a conserved motif "ATAGA + poly-T" as found in other lepidopteran insects. There are 20 intergenic regions and 11 overlapping regions, ranging from 1 to 53 bp and 1 to 9 bp, respectively. The A + T content is relatively high across the whole mitogenome. The optimal tree topologies of Noctuoidea were given by the dataset consisting of all 13 PCGs from five families (exclude Oenosandridae). Our trees suggested a topology of (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))) and identified that C. anastomosis belongs to Notodontidae.

[Medicinal mammals resources in Yancheng nature reserve, Jiangsu province].

A preliminary investigation of the medicinal mammals resources was carried out in Yancheng nature reserve, Jiangsu province, and the results are as follows: The medicinal mammals cover 18 species. Among them, 3 species are listed as the national key protection in China, 1 species is in category 1 and 2 species are in category 2. Ten species are listed in economic important category and in scientific research category. The result of the investigation revealed the situation of the medicinal mammals resources in Yancheng nature reserve, Jiangsu province, and the suggestions of protection and management about the medicinal mammals were proposed in this paper.