The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

The eyestalk of crustaceans, such as Macrobrachium nipponense, contains many neurosecretory hormones affecting the process of reproduction, molting, metabolism of glucose, and other functions. In this study, important metabolic pathways and candidate genes involved in male sexual development were selected from M. nipponense. The methodology involved performing long-read and next generation transcriptome sequencing of genes from the androgenic gland after eyestalk ablation. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation of both the single-side (SS) and double-side (DS) eyestalk, compared with the control group (CG). The long-read transcriptome generated 49,840 non-redundant transcripts. A total of 1319, 2092 and 4351 differentially expressed genes (DEGs) were identified between CG versus SS, SS versus DS and CG versus DS, respectively. These data indicated that ablation of the double-sided eyestalk played stronger regulatory roles than the single-side ablation on male sexual development in M. nipponense. This was consistent with the qPCR analysis. Cell Cycle, Cellular Senescence, Oxidative Phosphorylation, Glycolysis/Gluconeogenesis and Steroid Hormone Biosynthesis were the primary enriched metabolic pathways in all three comparisons, and the important genes from these metabolic pathways were also selected. qPCR permitted secondary confirmation of ten DEGs identified through RNA-seq. RNAi-mediated silencing analyses of Hydroxysteroid dehydrogenase like 1 (HSDL1) revealed that HSDL1 has a positive regulatory effect on testes development. This study provides valuable insight into male sexual development in M. nipponense, including metabolic pathways and genes, paving the way for advanced studies on male sexual development in this species and in other crustaceans.

Male oriental river prawns (Macrobrachium nipponense) grow faster than females, and therefore, reach larger sizes by harvest time. Histological observations have indicated that the sex-differentiation sensitive period (which includes the formation of the androgenic gland, the testis, and the ovary) is from post-larvae (PL) developmental stage for M. nipponense. In this study, we prepared four microRNA (miRNA) and mRNA libraries using samples collected from sex-differentiation sensitive period (PL7 to PL16) to perform RNA-sequencing for identifying sex-related candidate miRNAs, genes, and metabolic pathways. A total of nine intersection miRNAs were identified, of which three were highly expressed in the androgenic gland, and their expression was verified by quantitative Real-Time PCR (qPCR). These three miRNAs and their 11 predicted target genes may be strong candidates for sex-related miRNAs and sex-related genes in M. nipponense. Five vital sex-related metabolic pathways were also identified that may regulate other sex-differentiation and sex-determination mechanisms. Finding of the study provide important insights to enhance our understanding on sex-differentiation and sex-determination mechanisms for M. nipponense.

This study aims to describe the epidemiological characteristics of scrub typhus, detect the spatio-temporal patterns of scrub typhus at county level, and explore the associations between the environmental variables and scrub typhus cases in Anhui Province. Time-series analysis, spatial autocorrelation analysis, and space-time scan statistics were used to explore the characteristics and spatiotemporal patterns of the scrub typhus in Anhui Province. Negative binomial regression analysis was used to explore the association between scrub typhus and environmental variables. A total of 16,568 clinically diagnosed and laboratory-confirmed cases were reported from 104 counties of 16 prefecture-level cities. The number of female cases was higher than male cases, with a proportion of 1.32:1. And the proportion of cases over 65 years old was the highest, accounting for 33.8% of the total cases. Two primary and five secondary high-risk clusters were detected in the northwestern, northeastern, and central-eastern parts of Anhui Province. The number of cases in primary and secondary high-risk clusters accounted for 60.27% and 3.00%, respectively. Scrub typhus incidence in Anhui Province was positively correlated with the population density, normalized difference vegetation index, and several meteorological variables. The mean monthly sunshine duration with 3 lags (SSD_lag3), mean monthly ground surface temperature with 1 lag (GST_lag1), and mean monthly relative humidity with 3 lags (RHU_lag3) had the most significant association with increased cases of scrub typhus. Our findings indicate that public health interventions need to be focused on the elderly farmers in north of the Huai River in Anhui Province.

The influenza A (H7N9) subtype remains a public health problem in China affecting individuals in contact with live poultry, particularly at live bird markets. Despite enhanced surveillance and biosecurity at LBMs H7N9 viruses are now more widespread in China. This study aims to quantify the temporal relationship between poultry surveillance results and the onset of human H7N9 infections during 2013-2017 and to estimate risk factors associated with geographical risk of H7N9 human infections in counties in Southeast China. Our results suggest that poultry surveillance data can potentially be used as early warning indicators for human H7N9 notifications. Furthermore, we found that human H7N9 incidence at county-level was significantly associated with the presence of wholesale LBMs, the density of retail LBMs, the presence of poultry virological positives, poultry movements from high-risk areas, as well as chicken population density and human population density. The results of this study can influence the current AI H7N9 control program by supporting the integration of poultry surveillance data with human H7N9 notifications as an early warning of the timing and areas at risk for human infection. The findings also highlight areas in China where monitoring of poultry movement and poultry infections could be prioritized.

The oriental river prawn, Macrobrachium nipponense, is an important commercial aquaculture resource in China. During breeding season, short ovary maturation cycles of female prawns cause multi-generation reunions in ponds and affect the growth of females representing individual miniaturization (known as autumn -propagation). These reproductive characteristics pose problems for in large - scale farming. To date, the molecular mechanisms of reproduction regulation of M. nipponense remain unclear. To address this issue, we performed transcriptome sequencing and gene expression analyses of eyestalk and cerebral ganglia of female M. nipponense during breeding and non-breeding seasons. Differentially expressed gene enrichment analysis results revealed several important reproduction related terms and signaling pathways, such as "photoreceptor activity", "structural constituent of cuticle" and "G-protein coupled receptor activity". The following six key genes from the transcriptome were predicted to mediate environmental factors regulating reproduction of M. nipponense: neuroparsin, neuropeptide F II, orcokinin II, crustacean cardioactive peptide, pigment-dispersing hormone 3 and tachykinin. These results will contribute to a better understanding of the molecular mechanisms of reproduction of oriental river prawns. Further detailed functional analyses of the candidate reproduction regulation related neuropeptides are needed to shed light on the mechanisms of reproduction of crustacean.