Metagenomic next-generation sequencing vs. conventional detection methods for detecting the pulmonary infections.

OBJECTIVE: The absence of proper pathogen treatment in the early stages can result in missing out on treatment chances or the overuse of antibiotics, both of which are the primary factors behind fatalities caused by lung infections. In this study, we aimed to investigate the efficacy of metagenomic next-generation sequencing (mNGS) in comparison to conventional detection methods in detecting infectious pathogens. PATIENTS AND METHODS: In this retrospective study, the infection pathogens of 104 patients were examined, and 86 bronchoalveolar lavage fluid (BALF), eight pleural effusions, and ten sputum samples were collected. The conventional detection approaches and mNGS analysis were used to determine the infection pathogen profiles and their detection rates were analyzed. RESULTS: Our study showed that mNGS was more sensitive (89.42%) than the conventional detection methods (56.73%) (p < 0.001), with a 32.69% improvement in sensitivity. The efficacy of mNGS in detecting mixed infections was significantly higher than that of conventional detection methods, with a detection rate of 85.29% compared to 17.65% (p < 0.001). The study demonstrated that mNGS had a higher sensitivity than the conventional detection methods when it came to diagnosing pulmonary infections, making it a potentially useful tool for clinical diagnosis. CONCLUSIONS: Combining mNGS with other pathogenic detection techniques can be an effective way to increase the rate of detecting pulmonary infections, as well as to provide guidance for treatment adjustments. Furthermore, the timing of sample collection and antibiotic administration can influence the effectiveness of mNGS when used on BALF specimens.

[Investigation and analysis of underground noise in Sichuan coal mines].

Objective: To understand the harm degree of underground noise and provide basis for noise control. Methods: In November 2019, 13 typical coal mines in Sichuan Province were selected as the research objects, and a total of 1203 sites and 609 jobs of noise exposure were investigated. Results: The noise intensity P75 >80 dB (A) was measured. The noise intensity of the inspection place of the air compressor is >86 dB (A) , the noise intensity of the inspection place of the gas drainage and the operation place of the main fan is between 80-85 dB (A) . Conclusion: Besides the harm of dust, noise exposure should also be paid attention to, and the measures of sound absorption and sound insulation should be taken or personal protection should be strengthened.

[Exogenous CRX gene induces Müller cell-derived progenitors to differentiate into photoreceptors].

Objective: To investigate whether exogenous CRX gene would be able to induce Müller cells-derived progenitors to differentiate into photoreceptors. Methods: Experimental study. Müller cells-derived progenitors resulted from primary Müller cells isolated from KunMing mice(5-7 days old) and cultured in free-serum media. Markers of Müller cells(glutamine synthetase, GS and Vimentin) and stem cells (Nestin and Sox2) were analysed by immnocytochemical assays. The secondary passage progenitors were divided into three groups: (1)the control group; (2)the empty vector group was transfected with lentivirus GFP; (3)the treated group was transfected with lentivirus GFP-CRX. After differentiation for 7 days, 7 days after differentiation, the expression of markers of photoreceptors were analyzed by q-PCR and Western blot assay. Results: There were 96.03%±1.21% of Müllerz cells cultured in vitro were immunoreactive to both GS and Vimentin. The dedifferentiation cells expressed Nestin and Sox2. After 7 days of induction, Exogenous CRX induced Müller cell-derived progenitors to differentiate into rod-like cells showed appearance like neuron morphology. q-PCR demonstrated that mRNAs of CRX and Rhodopsin were upregulated greatly. CRX mRNA were 9 times (P<0.05) and Rhodopsin mRNA were 20 times (P<0.05). The difference between the control group and the empty vector group was not statistically significant. Western blot showed that the expression of CRX was upregulated significantly, and was 2.7 times(P<0.05). But expression of Rhodopsin was weak and was nearly not detected in the control group and empty vector group. The expression of S-opsin was not detected. Conclusion: CRX gene could induce the differentiation of Müller cell-derived progenitor into rod photoreceptors, indicating a new avenue to study müller cells as endogenous seed cells for retinal photoreceptor. (Chin J Ophthalmol, 2018, 54: 923-928).

Tissue- and breed-specific expression of the chicken fat mass- and obesity-associated gene (FTO).

The fat mass- and obesity-associated gene (FTO) is involved in energy metabolism, but little is known about the chicken FTO gene. The objective of the current study was to detect chicken FTO expression patterns in the hypothalamus, liver, and skeletal muscle during development, and analyze the effects of age and breed on FTO expression. Real-time quantitative polymerase chain reaction results revealed that chicken FTO mRNA was expressed in all of the tissues tested. Chicken FTO exhibited tissue- and breed-specific patterns in the recessive White Plymouth Rock chicken and the Qingyuan partridge chicken. The highest FTO expression level was in the hypothalami of 1-week-old chicks. FTO mRNA was expressed more in the breast muscles and livers of recessive White Plymouth Rock chickens than those of Qingyuan partridge chickens at 1 and 8 weeks of age. These results indicate that FTO probably plays a significant role in energy metabolism at 1 week old, when chicks have undergone metabolic adaptations from yolk dependence to the utilization of exogenous feed.

Upregulation of NRAMP1 mRNA confirms its role in enhanced host immunity in post-artificial infections of Salmonella enteritidis in chicks.

1. Salmonella enteritidis (SE) is reported as the most common food-borne pathogen transmitted through poultry products. The natural resistance-associated macrophage protein 1 (NRAMP1) is a candidate gene associated with SE-mediated immune response and is related to the phagocytosis of SE. In this study, the classical single-nucleotide polymorphism (SNP) G2357A in exon 8 of the NRAMP1 gene was detected. The expression of NRAMP1 mRNA was first investigated in heterophil granulocytes and spleen in chicks from two different Chinese native breeds at 1, 3 and 10 d post-infection. In addition, the association with the effect of SE challenge was identified. 2. The G2357A SNP showed no significant association with Salmonella natural infection in birds from two different Chinese native breeds. 3. The upregulation of NRAMP1 mRNA in heterophils and spleen was involved in the response to pathogenic SE colonisation during the acute infection period in chicks. The results suggest that genetics, age, gender and interactions among these factors play important roles in the modulation of NRAMP1 mRNA expression and copy number by SE-mediated immune response in different Chinese chickens. 4. In conclusion, the enhancement of host immunity mediated by the upregulation of NRAMP1 mRNA in heterophil granulocytes and spleen might be more obvious and earlier in the chicks resistant to infections with SE than in susceptible chicks.

Molecular characterization, expression, and functional analysis of NOD1 in Qingyuan partridge chicken.

Nucleotide-binding oligomerization domain-containing protein-1 (NOD1) is a cytoplasmic pattern recognition receptor (PRR) and a key member of the NOD-like receptor (NLR) family. It has been reported that NLRs recognize a variety of microbial infections to induce the host innate immune response via modulation of NF-κB signaling. However, no reports on chicken NOD1 have been reported to date. In the current study, the full-length cDNA sequence of NOD1 was cloned. The complete open reading frame of NOD1 contains 2856 bp and encodes a 951 amino acid protein. Structurally, it is comprised of one caspase recruitment domain at the N-terminus, seven leucine-rich repeat regions at the C-terminus, and one NACHT domain between the N and C-termini. Phylogenetic analyses showed that chicken NOD1 clusters with duck and turkey. Furthermore, tissue-specific expression analyses of chicken NOD1 were performed using quantitative reverse transcription-PCR. NOD1 is widely distributed in various tissues, with the highest expression observed in testes. Finally, induced expression of chNOD1 and its associated adaptor molecule receptor-interacting protein 2, as well as the effector molecule NF-κB, was observed following S. enterica serovar Enteritidis infection. These findings highlight the important role of chicken NOD1 in response to pathogenic invasion. The present study is the first report of the cloning, expression, and functional analysis of chicken NOD1 and provides the foundation for future research on the structure and function of chicken NOD1.

Association of chicken growth hormone polymorphisms with egg production.

Growth hormone (GH) has diverse functions in animals, together with other hormones from the somatotropic axis. Here, chicken GH (cGH) was investigated in recessive white chickens and Qingyuan partridge chickens as a candidate gene affecting egg production traits. Chicken egg production traits were studied in association with 4 selected single nucleotide polymorphisms (T185G, G662A, T3094C, and C3199T). Genotyping was performed by the polymerase chain reaction-ligase detection reaction method. T185G was significantly associated with the egg production traits of body weight at first egg (BW), egg weight at first egg (EW), and the total egg production of 300-day old birds (EN 300). T3094C was also significantly associated with certain egg production traits; however, it affected the 2 breeds differently. Haplotypes of the 4 single nucleotide polymorphisms were also significantly associated with egg production traits of chicken age at first egg laying, BW, EW, and EN 300. H1H6 was the most advantageous diplotype for egg production. We putatively concluded that polymorphisms in the cGH gene and its haplotypes could be used as potential molecular markers for egg production traits to enhance the breeding programs of indigenous chickens.

Molecular genetic diversity and maternal origin of Chinese black-bone chicken breeds.

Chinese black-bone chickens are valued for the medicinal properties of their meat in traditional Chinese medicine. We investigated the genetic diversity and systematic evolution of Chinese black-bone chicken breeds. We sequenced the DNA of 520 bp of the mitochondrial cyt b gene of nine Chinese black-bone chicken breeds, including Silky chicken, Jinhu black-bone chicken, Jiangshan black-bone chicken, Yugan black-bone chicken, Wumeng black-bone chicken, Muchuan black-bone chicken, Xingwen black-bone chicken, Dehua black-bone chicken, and Yanjin black-bone chicken. We found 13 haplotypes. Haplotype and nucleotide diversity of the nine black-bone chicken breeds ranged from 0 to 0.78571 and 0.00081 to 0.00399, respectively. Genetic diversity was the richest in Jinhu black-bone chickens and the lowest in Yanjin black-bone chickens. Analysis of phylogenetic trees for all birds constructed based on hyplotypes indicated that the maternal origin of black-bone chickens is predominantly from three subspecies of red jungle fowl. These results provide basic data useful for protection of black-bone chickens and help determine the origin of domestic chickens.

Transcriptional co-activator PGC-1α gene is associated with chicken skeletal muscle fiber types.

The peroxisome proliferators-activated receptor-γ coactivator-1α (PGC-1α) is a candidate gene for meat quality traits because of its prominent role in muscle fiber type switching and determination. We investigated the effects of the PGC-1α gene on chicken skeletal muscle fiber type switching and on other meat quality traits. Single nucleotide polymorphisms were detected by PCR-SSCP and DNA sequencing, and then genotyping was performed by PCR-ligation detection reaction methods. Skeletal muscle fiber types, intramuscular fat content, shear forces, and water loss rate of the gastrocnemius lateralis muscle were measured in Qingyuan Partridge chickens and Recessive White chickens. Four SNPs, C171T in exon2, C384T in exon3, G646A in exon5, and A948G in exon8 were detected. Marker-trait association analysis indicated that G646A polymorphism was associated with skeletal myofiber type and that H1 (CCAA) was the most advantageous haplotype for skeletal myofiber type. We concluded that polymorphisms of the PGC-1α gene and their haplotypes are associated with chicken skeletal myofiber type traits.

Assessment of in vivo estrogenic response and the identification of environmental estrogens in the Yangtze River (Nanjing section).

Environmental estrogens in the aquatic environment have been shown to be responsible for the feminization of fish. The estrogenic content of the Yangtze River (Nanjing section--referred to as the studied area herein) was assessed using a combination of bioassay and chemical analysis. The in vivo bioassay was conducted by exposing adult male goldfish (Carassius auratus) to different concentrations of river water (25%, 50% and 100%) sampled from three representative sections of the studied area. Chemical analysis of estrogens in water from the three representative sections was conducted using solid phase extraction-gas chromatograph (SPE-GC) detection. The assay showed significant serum vitellogenin (VTG) and 17beta-estradiol (E2) induction and gonad atrophy in the treated fish. The strength of in vivo estrogenic responses in the three representative sections is in the order of Jiangxinzhou section>Daqiao section>Sanchahe section. The result is consistent with the levels of water estrogens determined from the chemical analysis. Steroidal estrogens were the major causal agents responsible for the estrogenic responses in the Jiangxinzhou and Daqiao sections, while phenolic estrogens were the main contributors in the Sanchahe section. The results of these in vivo bioassay and chemical analysis demonstrate that fish in the Yangtze River are exposed to environmental estrogens and are at a risk of feminization.

Integrated biomarker response index for the assessment of environmental stress of the Yangtze River (Nanjing section).

In the present study, multibiomarker effects of the river water of three representative sections in Nanjing section of the Yangtze River were investigated in goldfish (Carassius auratus). The organic toxicants were extracted from the water samples using solid phase extraction. Acetylcholinesterase (AChE), glutathione-S-transferase (GST), 7-ethoxyresorufin-O-deethylase (EROD), glutathione peroxidase (GPx) and Na+/K+-ATPase activities were determined after exposure of the extracted components. The fractions of water samples from three sections (Daqiao, Sanchahe and Jiangxinzhou) altered these enzymatic activities. With the change of the extracts polarity, the levels of AChE, GST, EROD, Na+/K+-ATPase activities were different. The responses of enzymatic activities were mostly significant for those exposures of intermediate polar components (50-80% methanol extracts) and weakly polar components (ether and ether/hexane extracts). It has been shown that toxicants were mainly concentrated in these fractions in the Yangtze River (Nanjing section). With regard to response for different sections, EROD and GST activities seem to be more sensitive biomarkers. Integrated biomarker response index (IBR) were calculated and used to evaluate an integrated impact of pollutants from different sampling sections. The order of negative biological effects of the three sections was Jiangxinzhou>Sanchahe>Daqiao. The wild fish living in Nanjing section of the Yangtze River were at potential ecological risk.

Study on environmental estrogen pollution in Yangtze River (Nanjing section) by an in vivo bioassay.

Estrogenic activities and main causative fractions in three representative sections of Yangtze River (Nanjing section) were determined. The results showed that significant vitellogenin (VTG) and 17beta-estradiol (E(2)) induction and gonad atrophy were observed. Estradiol equivalents of actual water samples from Jiangxinzhou section, Sanchahe section and Daqiao section were 0.3651, 0.1301 and 0.5060 ng L(-1), respectively. Polar contaminants were responsible for the estrogenic activities in Jiangxinzhou section and Daqiao section while mid-polar and nonpolar contaminants resulted in majority of the estrogenic activity in Sanchahe section. To Jiangxinzhou section, Sanchahe section and Daqiao section, good positive correlations between VTG and E(2) (the correlation coefficients were 0.737, 0.690 and 0.817, respectively) and good inverse correlations between VTG and gonado-somatic index (GSI; the correlation coefficients were -0.838, -0.540 and -0.794, respectively) were obtained, whereas the correlations between E(2) and GSI were relatively poor (the correlation coefficients were only -0.557, -0.620 and -0.509, respectively).

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers.

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F-statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus. Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.

Evidence for the existence of an organ specific, androgen-independent pathway of progression in patients with metastatic prostate cancer.

Ample clinical and preclinical data support the central role of bone-epithelial interaction in the progression of prostate cancer. The clinical progression of prostate cancer has been partially attributed to a cascade of interactions between the cancer compartment and microenvironment compartments. The expression of prostate specific antigen (PSA) parallels the activity of the epithelial compartment of prostate cancer. However, the clinical study of the bone-epithelial interaction has been limited by the lack of accessible relevant human tissue for study. This study was designed (1) to assess the value of human bone marrow as a source of tissue to study the bone-epithelial interaction and (2) to determine whether bone marrow supernatant regulates the expression of PSA in a human prostate cancer cell line (LNCaP) in vitro. The acellular bone marrow supernatant derived from patients with prostate cancer with different degrees of tumor spread, hormonal status, and histology were assayed for their ability to induce PSA expression in a human LNCaP. The bone marrow supernatants were derived from 53 patients with prostate cancer (49 with adenocarcinoma and 4 with small cell carcinoma) and eight control patients, who had cancers in other sites. In addition, the match serum specimens derived from 25 of the study patients also had been assayed for its PSA inductivity. In addition to the comparison with "static" serum and BM concentration of PSA, the rate of significant PSA induction by clinical stage and hormonal status was assessed. Patients with androgen-independent disease had the highest rate of PSA-inducing ability. Only two patients (8%) had weak PSA-inducing ability from their serum (both with high volume disease) and none of the bone marrow supernatants derived from patients without prostate cancer or small cell carcinoma had inducing ability. No correlation between the static BM or serum PSA concentrations and the inducing ability was seen. These results indicate that PSA expression can be regulated by androgen-independent factors. The bone marrow supernatant of patients with prostate cancer has unique properties and is a valuable source of tissue for clinical study of the progression of prostate cancer. These preliminary data suggest that induction of PSA by bone marrow supernatant should be studied for its clinical utility as an assay for the interaction between the epithelial and bone compartments, and it supports the existence of androgen-independent pathways of PSA regulation by the bone marrow supernatant of patients with advanced prostate cancer. If confirmed, these findings would support the use of bone marrow supernatant to study the osseous specific progression of prostate cancer.

Activated production of metalloproteinases in Ki-ras-transformed human osteosarcoma cells.

The human osteosarcoma cell culture HOS does not produce matrix metalloproteinases (MPs). However, after transformation with the Ki-ras oncogene, the resulting culture (KHOS) produced readily detectable MPs. The molecular weight of the major MP was 66 kDa, while the molecular weights of two other minor bands were 71 kDa and 60 kDa. The activity of all three enzymes was inactivated by treatment with ethylene diaminetetra acetic acid, indicating that they are probably MPs. The substrate preference of the 66-kDa MP (in decreasing order) was gelatin and collagens V, I, III, and IV. Treatment of the MPs with p-aminophenylmercuric acetate led to the appearance of 62-kDa activated enzyme. The MP produced by KHOS cells did not react with the monoclonal anti-rat stromelysin antibody MC. Treatment of KHOS cells with retinoic acid and dexamethasone, which are known to suppress c-fos/c-jun and AP-1, suppressed the production of the MPs. Therefore, the activation of MPs by Ki-ras in KHOS cells may involve c-fos/c-jun and the AP-1-responsive pathway.