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Background: Bacillary dysentery caused by bacteria of the genus Shigella is a significant public health problem in developing countries such as China. The objective of this study was to analyze the epidemiological pattern of bacillary dysentery, the diversity of the causative agent, and the antimicrobial resistance patterns of Shigella spp. for the purpose of determining the most effective allocation of resources and prioritization of interventions., Methods: Surveillance data were acquired from the National Infectious Disease Information Reporting System (2004-2014) and from the sentinel hospital-based surveillance system (2005-2014). We analyzed the spatial and temporal distribution of bacillary dysentery, age and sex distribution, species diversity, and antimicrobial resistance patterns of Shigella spp., Results: The surveillance registry included over 3 million probable cases of bacillary dysentery during the period 2004-2014. The annual incidence rate of bacillary dysentery decreased from 38.03 cases per 100,000 person-years in 2004 to 11.24 cases per 100,000 person-years in 2014. The case-fatality rate decreased from 0.028% in 2004 to 0.003% in 2014. Children aged <1 year and 1-4 years were most affected, with higher incidence rates (228.59 cases per 100,000 person-years and 92.58 cases per 100,000 person-years respectively). The annual epidemic season occurred between June and September. A higher incidence rate of bacillary dysentery was found in the Northwest region, Beijing and Tianjin during the study period. Shigella flexneri was the most prevalent species that caused bacillary dysentery in China (63.86%), followed by Shigella sonnei (34.89%). Shigella isolates were highly resistant to nalidixic acid (89.13%), ampicillin (88.90%), tetracycline (88.43%), and sulfamethoxazole (82.92%). During the study period, isolates resistant to ciprofloxacin and cefotaxime increased from 8.53 and 7.87% in 2005 to 44.65 and 29.94% in 2014, respectively., Conclusions: The incidence rate of bacillary dysentery has undergone an obvious decrease from 2004 to 2014. Priority interventions should be delivered to populations in northwest China and to individuals aged <5 years. Antimicrobial resistance of Shigella is a serious public health problem and it is important to consider the susceptibility profile of isolates before determining treatment.

Background: Cross-border malaria transmission poses a challenge for countries to achieve and maintain malaria elimination. Because of a dramatic increase of cross-border population movement between China and 14 neighbouring countries, the malaria epidemic risk in China's land border regions needs to be understood., Methods: In this study, individual case-based epidemiological data on malaria in the 136 counties of China with international land borders, from 2011 to 2014, were extracted from the National Infectious Disease Information System. The Plasmodium species, seasonality, spatiotemporal distribution and changing features of imported and indigenous cases were analysed using descriptive spatial and temporal methods., Results: A total of 1948 malaria cases were reported, with 1406 (72.2%) imported cases and 542 (27.8%) indigenous cases. Plasmodium vivax is the predominant species, with 1536 malaria cases occurrence (78.9%), following by Plasmodium falciparum (361 cases, 18.5%), and the others (51 cases, 2.6%). The magnitude and geographic distribution of malaria in land border counties shrunk sharply during the elimination period. Imported malaria cases were with a peak of 546 cases in 2011, decreasing yearly in the following years. The number of counties with imported cases decreased from 28 counties in 2011 to 26 counties in 2014. Indigenous malaria cases presented a markedly decreasing trend, with 319 indigenous cases in 2011 reducing to only 33 indigenous cases in 2014. The number of counties with indigenous cases reduced from 26 counties in 2011 to 10 counties in 2014. However, several bordering counties of Yunnan province adjacent to Myanmar reported indigenous malaria cases in the four consecutive years from 2011 to 2014., Conclusions: The scale and extent of malaria occurrence in the international land border counties of China decreased dramatically during the elimination period. However, several high-risk counties, especially along the China-Myanmar border, still face a persistent risk of malaria introduction and transmission. The study emphasizes the importance and urgency of cross-border cooperation between neighbouring countries to jointly face malaria threats to elimination goals.

Background: MYB family proteins are one of the most abundant transcription factors in the cotton plant and play diverse roles in cotton growth and evolution. Previously, few studies have been conducted in upland cotton, Gossypium hirsutum. The recent release of the G. hirsutum genome sequence provides a great opportunity to identify and characterize the entire upland cotton MYB protein family., Results: In this study, we undertook a comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during cotton fiber development. A total of 524 non-redundant cotton MYB genes, among 1986 MYB and MYB-related putative proteins, were identified and classified into four subfamilies including 1R-MYB, 2R-MYB, 3R-MYB, and 4R-MYB. Based on phylogenetic tree analysis, MYB transcription factors were divided into 16 subgroups. The results showed that the majority (69.1 %) of GhMYBs genes belong to the 2R-MYB subfamily in upland cotton., Conclusion: Our comparative genomics analysis has provided novel insights into the roles of MYB transcription factors in cotton fiber development. These results provide the basis for a greater understanding of MYB regulatory networks and to develop new approaches to improve cotton fiber development.

Background: With the dramatic increase in international travel among Chinese people, the risk of malaria importation from malaria-endemic regions threatens the achievement of the malaria elimination goal of China., Methods: Epidemiological investigations of all imported malaria cases were conducted in nine provinces of China from 1 Nov, 2013 to 30 Oct, 2014. Plasmodium species, spatiotemporal distribution, clinical severity, preventive measures and infection history of the imported malaria cases were analysed using descriptive statistics., Results: A total of 1420 imported malaria cases were recorded during the study period, with P. falciparum (723 cases, 50.9 %) and P. vivax (629 cases, 44.3 %) being the two predominant species. Among them, 81.8 % of cases were in Chinese overseas labourers. The imported cases returned from 41 countries, mainly located in Africa (58.9 %) and Southeast Asia (39.4 %). About a quarter (25.5 %, 279/1094) of counties in the nine study provinces were affected by imported malaria cases. There were 112 cases (7.9 %) developing complicated malaria, including 12 deaths (case fatality rate: 0.8 %). Only 27.8 % of the imported cases had taken prophylactic anti-malarial drugs. While staying abroad, 27.7 % of the cases had experienced two or more episodes of malaria infection. The awareness of clinical manifestations and the capacity for malaria diagnosis were weak in private clinics and primary healthcare facilities., Conclusions: Imported malaria infections among Chinese labourers, returned from various countries, poses an increasing challenge to the malaria elimination programme in China. The risk of potential re-introduction of malaria into inland malaria-free areas of China should be urgently addressed.

Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum., Methods: The stem apexes of wild-type upland cotton (Ari971) and its dwarf mutant (Ari1327) and tall-culm mutant (Ari3697) at the fifth true leaf stage were extracted for RNA, respectively. Transcriptome and small RNA libraries were constructed and subjected to next generation sequencing., Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which was consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and pectate-lyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation., Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culm and dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.

Background: Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology., Results: We investigated two distinct salt stress phases--dehydration (4 h) and ionic stress (osmotic restoration; 24 h)--that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs., Conclusions: Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.

Hand, foot and mouth disease (HFMD), a common contagious disease that usually affects children, is normally mild but can have life-threatening manifestations. It can be caused by enteroviruses, particularly Coxsackieviruses and human enterovirus 71 (HEV71) with highly variable clinical manifestations. In the spring of 2008, a large, unprecedented HFMD outbreak in Fuyang city of Anhui province in the central part of southeastern China resulted in a high aggregation of fatal cases. In this study, epidemiologic and clinical investigations, laboratory testing, and genetic analyses were performed to identify the causal pathogen of the outbreak. Of the 6,049 cases reported between 1 March and 9 May of 2008, 3023 (50%) were hospitalized, 353 (5.8%) were severe and 22 (0.36%) were fatal. HEV71 was confirmed as the etiological pathogen of the outbreak. Phylogenetic analyses of entire VP1 capsid protein sequence of 45 Fuyang HEV71 isolates showed that they belong to C4a cluster of the C4 subgenotype. In addition, genetic recombinations were found in the 3D region (RNA-dependent RNA polymerase, a major component of the viral replication complex of the genome) between the Fuyang HEV71 strain and Coxsackievirus A16 (CV-A16), resulting in a recombination virus. In conclusion, an emerging recombinant HEV71 was responsible for the HFMD outbreak in Fuyang City of China, 2008.