[Molecular epidemiological characteristics of newly diagnosed HIV-1 cases in Fujian Province in 2020]

OBJECTIVE

To investigate the HIV-1 genotype and distribution of newly diagnosed HIV-1 cases in Fujian Province in 2020, so as to provide insights into formulation of the precise AIDS control strategy in the province.

METHODS

Newly diagnosed HIV-1 cases without antiretroviral therapy (excluding AIDS patients) were randomly sampled from each city of Fujian Province in 2020 at a proportion of 50% of the mean number of HIV-infected cases reported across 9 cities of Fujian Province during the past three years. Subjects' demographic and epidemiological data were collected and blood samples were collected. The HIV-1 pol gene was amplified using nested reverse-transcription PCR assay, and the gene sequences were used for HIV-1 genotyping and phylogenetic analysis. The gene sequences were uploaded to the HIV Drug Resistance Database (http://hivdb.stanford.edu) for genotypic drug resistance assays, and the scores and level of HIV drug resistance were estimated using the HIVDB Algorithm version 9.5.

RESULTS

A total of 1 043 newly diagnosed HIV-1 cases were reported in Fujian Province in 2020, and 936 gene sequences were successfully obtained following sequencing of blood samples. There were 9 HIV-1 genotypes characterized in blood samples from 936 newly diagnosed HIV-1 cases, with CRF07_BC (52.1%) and CRF01_AE (30.4%) as predominant subtypes, followed by CRF08_BC (4.9%), CRF55_01B (3.0%), subtype C (2.5%), subtype B (2.1%), CRF85_BC (1.7%), CRF59_01B (0.3%) and CRF65_CPX (0.1%), and unidentified subtypes were found in 26 blood samples. HIV-1 drug resistance was detected in 43 out of the 936 newly diagnosed HIV-1 cases, with 4.6% prevalence of HIV-1 drug resistance prior to therapy, and the highest drug resistance was found in the HIV CRF59_01B subtype, followed by in CRF08_BC, B, C, CRF01_AE, CRF07_BC and other subtypes, with a significant difference in the genotype-specific prevalence of HIV-1 drug resistance (χ2 = 45.002, P < 0.05).

CONCLUSIONS

There was a HIV-1 genotype diversity in Fujian Province in 2020, and emerging recombinant and drug-resistant HIV-1 strains were detected and spread across patients and regions. Monitoring of HIV-1 genotypes is recommended to be reinforced for timely understanding of the transmission and spread of novel recombinant and drug-resistant HIV-1 strains.

Gastrointestinal signet ring cell malignancy: current advancement and future prospects

Globally, gastrointestinal cancer is the most widespread neoplastic disease and the primary contributor to cancer-associated fatalities. Gastrointestinal signet ring cell carcinoma (SRCC) exhibits unique distinguishing features in several aspects when compared to adenocarcinomas (ACs). The scarcity of signet ring cell carcinoma has resulted in a heightened significance of related clinical and molecular investigations. However, a comprehensive and systematic review of the clinical, molecular, therapeutic, and research aspects of this disease is currently absent. This review provides an overview of the latest developments in our understanding of the clinical and molecular features of gastrointestinal signet ring cell carcinoma (SRCC). Additionally, we have compiled a list of potential therapeutic targets or biomarkers, as well as an examination of the current treatment options and the possible mechanisms of formation.

An unneglected source to ambient brown carbon and VOCs at harbor area: LNG tractor truck

The ambient air quality of harbors area in Asia is commonly more polluted compared to other continents. The airborne pollutant is directly or indirectly related to a significant impact of traffic emissions. This study for the first time assessed the impacts on brown carbon (BrC) and volatile organic compounds (VOCs) from in-port liquid natural gas (LNG) tractor truck at harbor areas, via conducting real-time monitoring of VOCs characteristic and sampling for ambient air at a harbor (named as W harbor) in Shanghai, China, collecting emissions of in-port LNG tractor truck and miniCast in laboratory, as well as statistics of external container diesel trucks in the port for further validation. HPLC/DAD/Q-Tof MS was adopted for sample analysis. Results showed that many CHO compounds were associated with vehicle exhausts. Among of them, aliphatic CHO compounds with low degree of unsaturation were identified as fatty acids and fatty acid methyl esters extensively existing in fuel combustion emissions. And non-aliphatic CHO compounds characterized by low O/C ratios (<0.17) identified for the harbor air came from the emissions of in-port LNG power trucks with low-speed driving and idling. The ambient average non-methane total hydrocarbons (NMHC) concentration (0.59 ppm) at W harbor was much greater than that for other areas in Shanghai. The higher ratios of toluene/benzene (3.30) and m/p-xylene/ethylbenzene (3.11) observed at W harbor implied instead of external container diesel trucks, the dominating contributing of internal LNG tractor trucks to ambient VOCs cannot be neglected. This study concluded that LNG is not as clean as it was expected. The LNG-fueled vehicles can produce strong light-absorption chromophores as well as high concentration of VOCs.

[Screening of pathogenic molecular markers of Staphylococcus aureus in children based on whole genome sequencing technology]

OBJECTIVES

To explore the molecular characteristics of Staphylococcus aureus (S. aureus) in children, and to compare the molecular characteristics of different types of strains (infection and colonization strains) so as to reveal pathogenic molecular markers of S. aureus.

METHODS

A cross-sectional study design was used to conduct nasopharyngeal swab sampling from healthy children in the community and clinical samples from infected children in the hospital. Whole genome sequencing was used to detect antibiotic resistance genes and virulence genes. A random forest method to used to screen pathogenic markers.

RESULTS

A total of 512 S. aureus strains were detected, including 272 infection strains and 240 colonization strains. For virulence genes, the carrying rates of enterotoxin genes (seb and sep), extracellular enzyme coding genes (splA, splB, splE and edinC), leukocytotoxin genes (lukD, lukE, lukF-PV and lukS-PV) and epidermal exfoliating genes (eta and etb) in infection strains were higher than those in colonization strains. But the carrying rates of enterotoxin genes (sec, sec3, seg, seh, sei, sel, sem, sen, seo and seu) were lower in infection strains than in colonization strains (P<0.05). For antibiotic resistance genes, the carrying rates of lnuA, lnuG, aadD, tetK and dfrG were significantly higher in infection strains than in colonization strains (P<0.05). The accuracy of cross-validation of the random forest model for screening pathogenic markers of S. aureus before and after screening was 69% and 68%, respectively, and the area under the curve was 0.75 and 0.70, respectively. The random forest model finally screened out 16 pathogenic markers (sem, etb, splE, sep, ser, mecA, lnuA, sea, blaZ, cat(pC233), blaTEm-1A, aph(3')-III, ermB, ermA, ant(9)-Ia and ant(6)-Ia). The top five variables in the variable importance ranking were sem (OR=0.40), etb (OR=3.95), splE (OR=1.68), sep (OR=3.97), and ser (OR=1.68).

CONCLUSIONS

The random forest model can screen out pathogenic markers of S. aureus and exhibits a superior predictive performance, providing genetic evidence for tracing highly pathogenic S. aureus and conducting precise targeted interventions.

BCR::ABL1-like acute lymphoblastic leukaemia: a single institution experience on identification of potentially therapeutic targetable cases

BACKGROUND

BCR::ABL1-like acute lymphoblastic leukaemia (BCR::ABL1-like ALL) is characterized by inferior outcomes. Current efforts concentrate on the identification of molecular targets to improve the therapy results. The accessibility to next generation sequencing, a recommended diagnostic method, is limited. We present our experience in the BCR::ABL1-like ALL diagnostics, using a simplified algorithm.

RESULTS

Out of 102 B-ALL adult patients admitted to our Department in the years 2008-2022, 71 patients with available genetic material were included. The diagnostic algorithm comprised flow cytometry, fluorescent in-situ hybridization, karyotype analysis and molecular testing with high resolution melt analysis and Sanger Sequencing. We recognized recurring cytogenetic abnormalities in 32 patients. The remaining 39 patients were screened for BCR::ABL1-like features. Among them, we identified 6 patients with BCR::ABL1-like features (15.4%). Notably, we documented CRLF2-rearranged (CRLF2-r) BCR::ABL1-like ALL occurrence in a patient with long-term remission of previously CRLF2-r negative ALL.

CONCLUSIONS

An algorithm implementing widely available techniques enables the identification of BCR::ABL1-like ALL cases in settings with limited resources.

Biological activity of recombinant bovine IFN-α and inhibitory effect on BVDV in vitro

Type I interferon has great broad-spectrum antiviral ability and immunomodulatory function, and its receptors are expressed in almost all types of cells. Bovine viral diarrhea virus (BVDV) is an important pathogen causing significant economic losses in cattle. In this study, a recombinant expression plasmid carrying bovine interferon-α(BoIFN-α)gene was constructed and transformed into E. coli BL21 (DE3) competent cells. SDS-PAGE and Westernblotting analysis showed that the recombinant BoIFN-α protein (rBoIFN-α) was successfully expressed. It is about 36KD and exists in the form of inclusion body. When denatured, purified and renatured rBoIFN-α protein stimulated MDBK cells, the expression of interferon stimulating genes (ISGs) such as ISG15, OAS1, IFIT1, Mx1 and IFITM1 were significantly up-regulated, and reached the peak at 12 h (P< 0.001). MDBK cells were infected with BVDV with moi of 0.1 and 1.0, respectively. The virus proliferation was observed after pretreatment with rBoIFN-α protein and post-infection treatment. The results showed that the denatured, purified and renatured BoIFN-α protein had good biological activity and could inhibit the replication of BVDV in MDBK cells in vitro, which provided a basis for BoIFN-α as an antiviral drug, immune enhancer and clinical application of BVDV.

BCR/ABL1-Like Acute Lymphoblastic Leukemia: From Diagnostic Approaches to Molecularly Targeted Therapy

BACKGROUND

BCR/ABL1-like acute lymphoblastic leukemia is a newly recognized high-risk subtype of ALL, characterized by the presence of genetic alterations activating kinase and cytokine receptor signaling. This subtype is associated with inferior outcomes, compared to other B-cell precursor ALL.

SUMMARY

The recognition of BCR/ABL1-like ALL is challenging due to the complexity of underlying genetic alterations. Rearrangements of CRLF2 are the most frequent alteration in BCR/ABL1-like ALL and can be identified by flow cytometry. The identification of BCR/ABL1-like ALL can be achieved with stepwise algorithms or broad-based testing. The main goal of the diagnostic analysis is to detect the underlying genetic alterations, which are critical for the diagnosis and targeted therapy.

KEY MESSAGES

The aim of the manuscript is to review the available data on BCR/ABL1-like ALL characteristics, diagnostic algorithms, and novel, molecularly targeted therapeutic options.

Spatial variation of dissolved organic nitrogen in Wuhan surface waters: Correlation with the occurrence of disinfection byproducts during the COVID-19 pandemic

Intensified sanitization practices during the recent coronavirus disease-2019 (COVID-19) led to the release of chlorine-based disinfectants in surface water, potentially triggering the formation of disinfection byproducts (DBPs) in the presence of dissolved organic nitrogen (DON). Thus, a comprehensive investigation of DON's spatial distribution and its association with DBP occurrence in the surface water is urgently needed. In this study, a total of 51 water samples were collected from two rivers and four lakes in May 2020 in Wuhan to explore the regional variation of nitrogen (N) species, DON's compositional characteristics, and the three classes of DBP occurrence. In lakes, 53.0% to 86.3% of N existed as DON, with its concentration varying between 0.3-4.0 mg N/L. In contrast, NO₃^--N was the dominant N species in rivers. Spectral analysis revealed that DON in the lakes contained higher humic and fulvic materials with higher A₂₅₄, A₂₅₃/A_203, SUVA₂₅₄, and P_III+IV/P_I+II+V ratios, while rivers had higher levels of hydrophilic compounds. Trihalomethanes (THMs) were the most prevalent DBPs in the surface waters, followed by N-nitrosamines and haloacetonitriles (HANs). The levels of N-nitrosamines (23.1-97.4 ng/L) increased significantly after the outbreak of the COVID-19 pandemic. Excessive DON in the surface waters was responsible for the formation of N-nitrosamines. This study confirmed that the presence of DON in surface water could result in DBP formation, especially N-nitrosamines, when disinfectants were discharged into surface water during the COVID-19 pandemic.

Histological diversity and molecular characteristics in gastric cancer: relation of cancer stem cell-related molecules and receptor tyrosine kinase molecules to mixed histological type and more histological patterns

BACKGROUND

Gastric cancers (GCs) are still one of the leading causes of cancer-related mortality. The histological and molecular features of GC may differ widely from area to area within the same tumor. Intratumoral heterogeneity has been considered a major obstacle to an efficient diagnosis and successful molecular treatment.

METHODS

We selected and reevaluated 842 GC cases and analyzed the relationship between numbers or composites of histological patterns within tumors, and clinicopathological parameters in mucosal and invasive areas. In addition, we searched for the GC-associated molecules or molecular subtypes marking histological diversities.

RESULTS

GC cases with more histological numbers or mixed types in invasive areas showed significantly higher T grade and staging, whereas those in mucosal areas did not show any significant associations. GCs with histological diversities showed poorer prognosis and characteristically expressed cancer stem cell-related molecules (CD44, CD133 or ALDH1) and receptor tyrosine kinase molecules (HER2, EGFR or c-MET) as well as Helicobacter pylori infection. Expressions of CD44, HER2, c-MET, laminin 5·2 or retained E-cadherin in mucosal areas were predictive of more histological numbers and mixed types in invasive areas. In addition, the chromosomal instability subtype of GC showed significant associations with more histological numbers and mixed histological type, whereas the genomic stability subtype of GC showed a significant relationship with pure type.

CONCLUSIONS

We displayed the relationship between histological diversity and molecular features in GC, and we hope that the present data can contribute to the early diagnosis and prevention, and effective treatment of GC.

Molecular characterization and antiparasitic activity analysis of a novel piscidin 5-like type 4 from Larimichthys crocea

Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture teleosts and cause high lethality and economic loss, especially Larimichthys crocea. Current methods of controlling or preventing this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. The antiparasitic activity of some antimicrobial peptides (AMPs) attracted extensive attention of scholars. In the study, a novel piscidin 5-like type 4 (termed Lc-P5L4) excavated from comparative transcriptome of C. irritans - immuned L. crocea was identified and characterized. Sequence analysis shows the full-length cDNA of Lc-P5L4 is 539 bp containing an open reading frame (ORF) of 198 bp which encodes a peptide of 65 amino acid residues. The genome consists of three exons and two introns which exist in its ORF, and all the exon-intron boundaries are in accordance with classical GT-AG rule (GT/intron/AG). Multiple alignments indicate the signal peptides share highly conserved identity, while mature peptides are more diverse. Phylogenetic analysis displays Lc-P5L4 clusters together with other members of piscidin 5-like family. Next, quantitative Real-time PCR (qRT-PCR) detection found C. irritans infection could upregulate Lc-P5L4 expression level in all tested tissues significantly, it appeared earliest upregulation in the theronts infection stage in the head kidney; the expression contents reached to maximum level in the intestine, gill and muscle during trophonts falling off stage; while it was just upregulated during secondary bacterial infection stage in the liver and spleen. The data showed Lc-P5L4 upregulation time points were in accordance with different infection stages. With recombinant Lc-P5L4 (rLc-P5L4) obtained through Escherichia coli system, in vitro assay showed rLc-P5L4 could cause cilia deactivation, cell bodiesclumping and sticking to each other, then cell membrane rupture and contents leakage. The data illustrated Lc-P5L4 played critical roles in the immune defense against C. irritans infection, and provided another proof that piscidins exhibit multiple anti- C. irritans features.

The characterization of dissolved organic matter in alkaline fermentation of sewage sludge with different pH for volatile fatty acids production

Sewage sludge (SS) alkaline fermentation (especially at pH 10) can efficiently enhance volatile fatty acids (VFAs) production. VFAs are considered an excellent carbon source for the biological nutrient removal (BNR) process. Dissolved organic matter (DOM) in fermentation liquid is the direct substrate used for producing VFAs and can greatly influence the effluent quality of BNR process. However, knowledge of DOM characteristics in sludge alkaline fermentation is limited. This study focused on the functional groups, fluorescent components and molecular features of DOM as well as molecular weight of proteins in SS alkaline fermentation (at pH uncontrolled, 7, 8, 9 and 10). Results showed a significantly improved generation of tryptophan-like and tyrosine-like substances as well as molecular weight <1 kDa proteins (381.5 ± 38.4 mg/L) was observed at pH 10 (p < 0.05). Further analysis of DOM molecular characteristics indicated that pH 10 resulted in the highest molecular diversity and the generation or degradation of easily biodegradable lipid-like and proteins/amino sugars-like formulas. The improved solubilization of DOM contributed to VFAs production. Meanwhile, increasing pH to 10 also promoted the release of hard-biodegradable organic matter, e.g., humic-like and lignin-like substances. Additionally, a high diversity of resistant N-containing organic molecules was generated at pH 10. Fermentation of SS at pH 10, is favored to enhance VFAs production and, can also result in a higher content of refractory DOM. This study helps to achieve a comprehensive understanding of SS alkaline fermentation and provides fundamental information for further treatment.

Full genome sequence analysis of a 1-7-4-like PRRSV strain in Fujian Province, China

PRRS virus (PRRSV) has undergone rapid evolution and resulted in immense economic losses worldwide. In the present study, a PRRSV strain named FJ0908 causing high abortion rate (25%) and mortality (40%) was detected in a swine herd in China. To determine if a new PRRSV genotype had emerged, we characterized the genetic characteristics of FJ0908. Phylogenetic analysis indicated that FJ0908 was related to 1-7-4-like strains circulating in the United States since 2014. Furthermore, the ORF5 sequence restriction fragment length polymorphism (RFLP) pattern of FJ0908 was 1-7-4. Additionally, FJ0908 had a 100 aa deletion (aa329-428) within nsp2, as compared to VR-2332, and the deletion pattern was consistent with most of 1-7-4 PRRSVs. Collectively, the data of this study contribute to the understanding of 1-7-4-like PRRSV molecular epidemiology in China.

Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017

OBJECTIVE

To investigate the evolutionary dynamics and characteristic of the molecular transmission networks of HIV-1 CRF01_AE in Nanjing.

METHODS

Viral samples were collected from 580 newly diagnosed HIV-1-infected patients. HIV-1 pol sequences were obtained and used for for molecular evolutionary analyses. The ML trees were constructed by MEGA 6.0 using under GTR+ G + I model with 1000 bootstrap replicates. The emergence and estimation of tMRCA and the evolutionary rate of the different CRF01_AE clusters were inferred using Bayesian phylogenetic analysis approaches implemented in the BEAST package. Pairwise genetic distances were calculated under the Tamura-Nei 93 model, a genetic distance threshold of ≤1.2% was used to identify potential transmission clusters. Network diagrams were plotted using Cytoscape 3.3.0.

RESULTS

Of these HIV-1-infected patients, 551 (91.5%) were males. The largest number of infections were attributed to homosexual (462, 79.7%). A total of 518 full-length pol genes were successfully amplified, based on the phylogenetic analysis CRF01_AE was the most predominantly circulating strain (45.0%, 233/518). As shown in the ML tree, three distinct clusters were observed. The 'Nanjing lineage' 1, 2, 3 has an estimated tMRCA around1996.61, 1993.61, 1984.61 respectively. Of 233 Nanjing sequences, 123 (55.2%) distributed in 30 molecular clusters, average Links/node was 7.8 with range (1-33), most of Nanjing strains shared links with local strains.

CONCLUSION

HIV-1 CRF01_AE was the most predominantly circulating strain, the epidemic of CRF01_AE in Nanjing was driven by multiple clusters of HIV-1 strains, and most CRF01_AE stains in our study were estimated to have originated in China in the 1990s.

[Molecular characteristics of serogroup B neisseria meningitidis, China]

Objective: To investigate the molecular characteristics of serogroup B neisseria meningitidis in China. Methods: Total of 485 (100 strains isolated from cerebrospinal fluid or blood samples of encephalomyelitis cases, and 385 strains isolated from nasopharynx of healthy carriers) Meningococcal serogroup B (MenB) strains, isolated from 29 provinces of China between 1968 and 2016, were analyzed by multilocus sequence typing (MLST) and PorA typing methods. Further, the genetic diversity of three MenB vaccine proteins, FHbp, NadA and NHBA, were analyzed. Results: The 485 study strains belonged to 270 sequence types (STs), 107 of which (representing 211 strains) could be grouped into ten clonal complexes (CC). CC4821 has been the predominant lineage in China since 2005 (28.7%, n=139). The most common PorA types of MenB strains from invasive meningococcal cases were P1.5-2,2-2 (10.0%, n=10), P1.5-1,2-2 (9.0%, n=9) and P1.5-1,10-4 (9.0%, n=9). Four hundred and twenty one strains had intact fhbp gene; variant 1, 2 and 3 accounted for 12.8% (54 strains), 85.0% (358 strains) and 2.2% (9 strains) respevtively. Ten out of 432 strains (2.3%) contained complete nadA gene. All the 172 strains for which the nhba gene was sequenced had intact gene sequence which corresponded to 68 peptide types. Conclusion: CC4821 was the predominant CC of MenB strains in China; the vaccine proteins were diverse about the sequences. The vaccine proteins should be carefully selected when developing MenB vaccines in China.

[Genetic characteristics of hemagglutinin and neuraminidase of avian influenza A (H7N9) virus in Guizhou province, 2014-2017]

Objective: To understand the molecular characteristics of hemagglutinin (HA) and neuraminidase (NA) as well as the disease risk of influenza virus A H7N9 in Guizhou province. Methods: RNAs were extracted and sequenced from HA and NA genes of H7N9 virus strains obtained from 18 cases of human infection with H7N9 virus and 6 environmental swabs in Guizhou province during 2014-2017. Then the variation and the genetic evolution of the virus were analyzed by using a series of bioinformatics software package. Results: Homology analysis of HA and NA genes revealed that 2 strains detected during 2014-2015 shared 98.8%-99.2% and 99.2% similarities with vaccine strains A/Shanghai/2/2013 and A/Anhui/1/2013 recommended by WHO, respectively. Two strains detected in 2016 and 14 strains detected in 2017 shared 98.2%-99.3% and 97.6%-98.8% similarities with vaccine strain A/Hunan/02650/2016, respectively. Other 6 stains detected in 2017 shared 99.1%-99.4% and 98.9%-99.3% similarities with strain A/Guangdong/17SF003/2016, respectively. Phylogenetic analysis showed that all the strains were directly evolved in the Yangtze River Delta evolution branch, but they were derived from different small branch. PEVPKRKRTAR↓GLF was found in 6 of 24 strains cleavage site sequences of HA protein, indicating the characteristic of highly pathogenic avian influenza virus. Mutations A134V, G186V and Q226L at the receptor binding sites were found in the HA. All the strains had a stalk deletion of 5 amino acid residue "QISNT" in NA protein, and drug resistance mutation R294K occurred in strain A/Guizhou-Danzhai/18980/2017. In addition, potential glycosylation motifs mutations NCS42NCT were found in the NA of 9 of 24 strains. Conclusions: HA and NA genes of avian influenza A (H7N9) virus showed genetic divergence in Guizhou province during 2014-2017. The mutations of key sites might enhance the virulence of the virus, human beings are more susceptible to it. Hence, the risk of infection is increasing.

Effect of mixing intensity on hydrolysis and acidification of sewage sludge in two-stage anaerobic digestion: Characteristics of dissolved organic matter and the key microorganisms

Mixing should be optimized in anaerobic digestion (AD) systems to achieve excellent biomaterials production in the sewage sludge (SS) management in wastewater treatment plant. AD depends on the coordinated activity of hydrolysis, acidification and methanogenesis. However, the effect of mixing intensity on characteristics of hydrolysis and acidification in AD of SS is still poorly understood. This study focused on the mixing intensity (30, 60, 90 and 120 rpm) effect on the characteristics of dissolved organic matter (DOM) and the key microorganisms in the hydrolysis and acidification of SS. Results showed that enhanced hydrolysis and acidification efficiency was obtained at mixing of 90 and 120 rpm (p < 0.05), while the maximum acetic acid (388 ± 21 mg/L) was produced at 90 rpm. Mixing at 90 rpm enhanced the release of protein and polysaccharide as well as humic acid. Further analyses of DOM molecular features revealed that 90 rpm led to the highest molecular diversity and easily biodegradable molecules (lipid and proteins/amino sugars), which contributed to the maximum hydrolysis and acidification efficiency. Firmicutes and Actinobacteria significantly increased with mixing intensity (p<0.05), and Chloroflexi and Fusobacteria were enriched at mixing of 90 rpm, which favored the hydrolysis of SS. The enrichment of Clostridium XI and Clostridium sensu stricto contributed to the acidification of DOM at 90 and 120 rpm. The results of this study can advance our knowledge about mixing intensity effects on the AD systems of SS. This research also showed how increasing mixing intensity to a relatively high speed can enhance the hydrolysis and acidification efficiency of SS.

Emergence of novel porcine reproductive and respiratory syndrome viruses (ORF5 RFLP 1-7-4 viruses) in China

Porcine reproductive and respiratory syndrome viruses (PRRSVs) pose a serious threat to the porcine industry of China, and the importation of novel strain(s) makes it challenging to control these viruses. Several NADC30-like PRRSV outbreaks have occurred in mainland China since 2013. In the current study, we report two novel PRRSVs, designated LNWK96 and LNWK130, which belong to lineage 1 and are closely related to US strains with ORF5 restriction fragment length polymorphism (RFLP) 1-7-4. The two viruses had a 100-aa deletion in the nsp2 gene corresponding to positions 328-427 in the VR-2332 strain, which was consistent with most of the ORF5 RFLP 1-7-4 viruses. Recombination analyses indicated that both viruses derived from the recombination of 1-7-4 isolates and ISU30 or NADC30, which were isolated in the United States. Taken together, these results demonstrate the emergence of ORF5 RFLP 1-7-4-like (NADC34-like) PRRSVs in China for the first time.

Genetic diversity among Trypanosoma vivax strains detected in naturally infected cattle in Nigeria based on ITS1 of rDNA and diagnostic antigen gene sequences

Trypanosoma vivax (sub-genus Duttonella) is largely responsible for non profitable livestock production in sub-Sahara Africa. In Nigeria, no study has addressed the molecular characteristic of T. vivax except Y486. Hence, we characterized and assessed the genetic diversity among T. vivax detected in naturally infected cattle in Nigeria using internal transcribed spacer 1 (ITS1) of ribosoma DNA (rDNA) and diagnostic antigen gene (DAG) sequences. The length of ITS1 and DAG sequences range from 215-220 to 257-338 bp, respectively and the mean G-C contents were 60 and 61.5 %. Homology search revealed 93-99 and 95-100 % homologies to T. vivax DAG and ITS1 sequences from GenBank. Aligned sequences revealed both ITS1 rDNA and DAG to be less polymorphic but DAG sequences of the Y486 strain and its clone showed marked variation from autochthonous strains. Phylogenetic analysis yielded tree that grouped T. vivax ITS1rDNA gene and DAG sequences into two main clades each. Considering the ITI1 rDNA sequences, clade A contained autochthonous T. vivax within which the South American sequences clustered, clade B contained the sequences of T. vivax from East Africa. Analysis of DAG revealed that the clade A contains autochthonous T. vivax sequences but clade B contained the Y486 and its clones. In conclusion, the diagnostic antigen gene sequences of the T. vivax detected in this study may have undergone considerable gene recombination through time and suggests that more than one strain of T. vivax exist among cattle population in Nigeria.

Molecular characterization and biological activity of bovine interferon-omega3

Bovine interferon-omega3 (BoIFN-ω3) gene was amplified from bovine liver genomic DNA, which encodes a 195-amino acid protein containing a 23-amino acid signal peptide. Analysis of the molecular characteristics revealed that BoIFN-ω3 evolving from IFN-ω, contained four cysteine residues and five alpha helices, showing that BoIFN-ω3 presented the typical molecular characteristics of type I interferon. BoIFN-ω3 exhibited antiviral and antiproliferative activities, which exerted a protective effect against VSV in several mammalian cell lines, as well as against BEV, IBRV, and BVDV in MDBK cell. Moreover, BoIFN-ω3 was shown to be highly sensitive to trypsin, but remaining stable despite changes in pH and temperature. Additionally, BoIFN-ω3 induced the transcription of Mx1, ISG15, and ISG56 genes, as well as the expression of Mx1 protein in a time-dependent manner. These findings will be useful to further study BoIFN-ω in host's defence against infectious diseases, particularly viral infections. Furthermore, results will facilitate further research on the bovine interferon family.

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BoIFN-ω3 presents antiviral activity on several mammalian cell lines and protective effect against VSV, BEV, IBRV, and BVDV.

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BoIFN-ω3 exhibits antiproliferative activity and insensitivity to pH and temperature.

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BoIFN-ω3 can activate the transcription of ISGs gene, as well as the expression of Mx1 in a time-dependent manner.

Molecular characteristics of lysozyme G in Euryglossa orientalis; cDNA cloning, phylogenic analysis, physicochemical properties and tissue gene expression

Lysozymes are the key molecules of innate immune system against bacterial infections. In the present study, we identified the molecular characteristics, physicochemical properties, antibacterial activity, evolutionary relationship and tissue expression pattern of g-type lysozyme in Euryglossa orientalis (EuOr LysG). The full-length EuOr LysG cDNA is composed of 588 nucleotides and an open reading frame encoding a protein with 195 amino acids with more than 65 % identity to g-type lysozyme of Solea senegalensis (73 %) and Scophthalmus rhombus (64 %). Amino acid sequence alignment showed that EuOr LysG protein possessed a conserved catalytic motif (Glu71-Asp84-Asp101) and one predicted disulfide bond between Cys32 and Cys122. Phylogenetic analysis based on the g-type lysozyme sequences indicated that E. orientalis and other fish of Pleuronectiformes were diverged together in the evolutionary history. The K _m and V _max values of the recombinant EuOr LysG were 0.266 mg/ml of Micrococcus lysodeikticus as substrate and 667 U/mg of protein, respectively. The optimum temperature and pH of recombinant EuOr LysG were 45 and 6 °C, respectively. Real-time PCR analysis showed that EuOr LysG transcript was most abundant in head kidney and gill and less in muscle. We also showed that the EuOr LysG had potent lytic activity against major fish bacterial pathogens with the highest activity against Bacillus cereus and Aeromonas hydrophila. Bacterial challenge with Vibrio parahaemolyticus could upregulate LysG in immune-related tissues. Our results help to understand the molecular and physicochemical characteristics of g-type lysozyme in E. orientalis which might play an important role in host defense against the bacterial infection.

Antimicrobial susceptibility, virulence determinant carriage and molecular characteristics of Staphylococcus aureus isolates associated with skin and soft tissue infections

A better understanding of the antimicrobial susceptibility, carriage of virulence determinants and molecular characteristics of Staphylococcus aureus isolates associated with skin and soft tissue infections (SSTIs) may provide further insights related to clinical outcomes with these infections. From January 2012 to September 2013, a total of 128 non-duplicate S. aureus isolates were recovered from patients with SSTIs. All 128 S. aureus SSTI isolates carried at least five virulence genes tested. Virulence genes detected among at least 70% of all tested isolates included hld (100%), hla (95.3%), icaA (96.9%), clf (99.2%), sdrC (79.7%), sdrD (70.3%), and sdrE (72.7%). The prevalence of MRSA isolates with 10 virulence genes tested (54.4%, 31/56) was significantly higher than that among MSSA isolates (35.2%, 25/71) (p < 0.05). The positive rates of seb, sen, sem, sdrE and pvl among MRSA isolates were significantly higher than among MSSA isolates (p < 0.05). ST7 and ST630 accounting for 10.9% were found to be the predominant STs. The most prevalent spa type was t091 (8.6%). MRSA-ST59-SCCmec IV was the most common clone (12.3%) among MRSA isolates whereas among MSSA isolates the dominant clone was MSSA-ST7 (15.5%). Six main clonal complexes (CCs) were found, including CC5 (52.3%), CC7 (11.7%), CC59 (8.6%), CC88 (6.3%), CC398 (4.7%), and CC121 (3.1%). A higher carriage of seb and sec was found among CC59 isolates. In comparison to CC5 and CC7 isolates, those with the highest carriage rates (>80.0%) of sdrC and sdrD, CC59 isolates had lower prevalence of these two virulence genes. All CC59 isolates were susceptible to gentamicin and trimethoprim/sulfamethoxazole, while CC5 and CC7 isolates had resistance rates to these two antimicrobials of 25.4% and 20.9%, and 40.0% and 40.0%, respectively. The resistance rates for tetracycline, clindamycin, and erythromycin among CC5 isolates were lower than among CC7 and CC59 isolates. In conclusion, the molecular typing of S. aureus SSTI isolates in the present study showed considerable heterogeneity. ST7 and ST630 became prevailing clones. Different S. aureus clones causing SSTIs were associated with specific antimicrobial resistance and virulence gene profiles.