Analysis of differentially expressed proteins after EHP-infection and characterization of caspase 3 protein in the whiteleg shrimp (Litopenaeus vannamei).

Whiteleg shrimp (Litopenaeus vannamei) is the most important species of shrimp farmed worldwide in terms of its economic value. Enterocytozoon hepatopenaei (EHP) infects the hepatopancreas, resulting in the hepatopancreatic microsporidiosis (HPM) of the host, which causes slow growth of the shrimp and poses a threat to the farming industry. In this study, differentially expressed proteins (DEPs) between EHP-infected and uninfected shrimp were investigated through proteomics sequencing. A total of 9908 peptides and 2092 proteins were identified. A total of 69 DEPs were identified in the hepatopancreas (HP), of which, 28 were upregulated and 41 were downregulated. Our results showed that the differences among the level of multiple proteins involved in the apoptosis were significant after the EHP infection, which indicated that the apoptosis pathway was activated in whiteleg shrimp. In addition, expression leve of caspase 3 gene were identified related to the EHP infection. Furthermore, predictions of spatial structure, analysis of phylogeny and chromosome-level linearity of the caspase 3 protein were performed as well. In conclusion, a relatively complete proteomic data set of hepatopancreas tissues in whiteleg shrimp were established in this study. Findings about genes involved in the apoptosis here will provide a further understanding of the molecular mechanism of EHP infection in the internal immunity of whiteleg shrimp.

Pathogen of Vibrio harveyi infection and C-type lectin proteins in whiteleg shrimp (Litopenaeus vannamei).

Diseases caused by Vibrio harveyi in shrimps have gradually become one group of the most serious threats to shrimp production, while related molecular mechanisms of infections with Vibrio harveyi are still not known well in shrimps. Here, we performed proteomic sequencing of hepatopancreas in whiteleg shrimps (Litopenaeus vannamei) infected with exogenous Vibrio harveyi, and subsequent functional annotation and calculation of differentially expressed proteins (DEPs) in this study. A total of 145 DEPs were obtained, among them 36 were up-regulated and 109 were down-regulated after the infection. Meanwhile, our results showed that after the infection of Vibrio harveyi, expression levels of a variety of C-type lectins (CTLs) were changed significantly. In-depth functional domain analysis and spatial structure prediction of these CTLs revealed that amino acid sequences and spatial structures of the C-type lectin domain (CTLD) shared by the CTL-S and IML proteins were variant, suggesting differential functions between the two CTLs. In summary, various members of the CTL family have different epidemic responses to Vibrio harveyi infection, which provides a theoretical guidance for deep-going investigations on practical immunity reactions and pathogen infections in shrimps.

Toll protein family structure, evolution and response of the whiteleg shrimp (Litopenaeus vannamei) to exogenous iridescent virus.

Whiteleg shrimp is a widely cultured crustacean, but frequent disease outbreaks have decreased production and caused significant losses. Toll-like receptors (TLRs) comprise a large innate immune family that is involved in the innate immune response. However, understanding of their regulatory mechanism is limited. In this study, PacBio sequencing and Illumina sequencing were applied to the gill and hepatopancreas tissues of whiteleg shrimp and an integrated transcript gene set was established. The upregulation of Toll1, Toll2 and Toll3 transcripts in the hepatopancreas tissue of whiteleg shrimp after iridescent virus infection implies that these proteins are involved in the immune response to the virus; simultaneously, the TRAF6 and relish transcripts in the Toll pathway were also upregulated, implying that the Toll pathway was activated. We predicted the three-dimensional structure of the five Toll proteins in whiteleg shrimp and humans and constructed a phylogenetic tree of the Toll protein family. In addition, there was a large discrepancy of Toll1 between invertebrates and vertebrates, presumably because of the loss of Toll1 protein sequence during the evolution process from invertebrates to vertebrates. Our research will improve the cognition of Toll protein family in invertebrates in terms of evolution, structure and function and provide theoretical guidance for researchers in this field.

Complete mitochondrial genome of sculptured slipper lobster Parribacus antarcticus (Lund, 1793).

We first determined and characterized the complete mitochondrial genome of Parribacus antarcticus. It is 15,806 bp long and consists of 22 tRNA, 2 rRNA, 13 protein-coding genes (PCGs), and 1 control region. The nucleotide composition is significantly biased with AT contents of 69.3%. Five PCGs used an unusual initiation codon, and nine PCGs were terminated with an incomplete or abnormal stop codon. Three microsatellites were identified and located in the ND 4 gene and D-loop region. Phylogenetic tree showed that P. antarcticus was first clustered with Ibacus ciliatus and Ibacus alticrenatus, which is consistent with the expected phylogenetic relationship.

Complete mitochondrial genome of blunt slipper lobsters Scyllarides squammosus (H. Milne Edwards, 1837).

The complete mitochondrial genome of Scyllarides squammosus was first determined and characterized. With a length of 15,644 bp, it consists of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 1 control region. The nucleotide composition is significantly biased with AT contents of 65.6%. Among these PCGs, five of them used an unusual initiation codon, and nine genes ended with an incomplete or abnormal stop codon. Two microsatellites were identified and located in COX3 gene and D-loop region. Phylogenetic analysis demonstrated that S. squammosus was first clustered with Scyllarides latus, which was consistent with the previous work.

The complete mitochondrial genome of rubble crab Daldorfia horrida (Linnaeus, 1758) using next-generation sequencing.

In this study, the complete mitochondrial genome of the rubble carb Daldorfia horrida was determined using Illumina next-generation sequencing. The circular mitogenome is 15,737 bp, with 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and one control region. The base composition is significantly biased (A, G, T, and C was 35.5%, 10.2%, 34.9%, and 19.4%, respectively) with A + T contents of 70.4%. Five microsatellites were identified in the mitogenome located in ND1, ND4, 16S genes and D-loop region. Phylogenetic tree showed that D. horrida is first clustered with Pseudocarcinus gigas and Myomenippe fornasinii, which revealed that Parthenopoidea has a close affinity with Eriphioidea in Heterotremata.

Characterization of complete mitochondrial genome of seven-eleven crab Carpilius maculatus (Linnaeus, 1758).

In this study, we first determined and characterised the complete mitochondrial genome of seven-eleven crab Carpilius maculatus from South China Sea. The C. maculatus mitogenome is 15,761 bp long, and consists of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. The nucleotide composition of C. maculatus mitogenome is significantly biased (A, G, T, and C was 35.9%, 9.8%, 35.5%, and 18.9%, respectively) with A + T contents of 71.3%. Three PCGs used an unusual initiation codon, and four PCGs were terminated with an uncomplete or abnormal stop codon. Six microsatellites were identified in C. maculatus mitogenome sequences. Phylogenetic tree showed that C. maculatus formed monophyletic clade with other Heterotremata species.

A peripheral component interconnect express-based scalable and highly integrated pulsed spectrometer for solution state dynamic nuclear polarization.

High sensitivity, high data rates, fast pulses, and accurate synchronization all represent challenges for modern nuclear magnetic resonance spectrometers, which make any expansion or adaptation of these devices to new techniques and experiments difficult. Here, we present a Peripheral Component Interconnect Express (PCIe)-based highly integrated distributed digital architecture pulsed spectrometer that is implemented with electron and nucleus double resonances and is scalable specifically for broad dynamic nuclear polarization (DNP) enhancement applications, including DNP-magnetic resonance spectroscopy/imaging (DNP-MRS/MRI). The distributed modularized architecture can implement more transceiver channels flexibly to meet a variety of MRS/MRI instrumentation needs. The proposed PCIe bus with high data rates can significantly improve data transmission efficiency and communication reliability and allow precise control of pulse sequences. An external high speed double data rate memory chip is used to store acquired data and pulse sequence elements, which greatly accelerates the execution of the pulse sequence, reduces the TR (time of repetition) interval, and improves the accuracy of TR in imaging sequences. Using clock phase-shift technology, we can produce digital pulses accurately with high timing resolution of 1 ns and narrow widths of 4 ns to control the microwave pulses required by pulsed DNP and ensure overall system synchronization. The proposed spectrometer is proved to be both feasible and reliable by observation of a maximum signal enhancement factor of approximately -170 for (1)H, and a high quality water image was successfully obtained by DNP-enhanced spin-echo (1)H MRI at 0.35 T.