[Whole genome sequencing reveals the distribution of resistance and virulence genes of pathogenic Escherichia coli CCHTP from giant panda].

Pathogenic Escherichia coli (E. coli) is the most common pathogen causing urinary tract infection in animals. We investigated the antibiotic resistance and virulence genes of pathogenic E. coli CCHTP derived from urine with occult blood of the giant panda by whole genome sequencing. The flanking sequencing of resistance and virulence genes in genomic islands were also analyzed. Our results demonstrate that E. coli CCHTP contains different families of antibiotic resistance genes, most of which are efflux pump related genes, including multiple drug resistance efflux pump genes mdfA, emrE, and mdtN. A total of 166 virulence factors and 563 virulence genes were identified, and the most virulence factors and related genes are involved in host cell attachment and invasion processes. Furthermore, sequence analysis of 19 genomic islands revealed that antibiotic and virulence genes are associated with mobile genetic elements (transposon and insertion sequence) in GIs011 and GIs017. These structures can mediate horizontal transfer of antibiotic and virulence genes. Our work described the distribution of antibiotic resistance genes and virulence genes in E. coli CCHTP, which may provide an important guidance for treatment and rational drug use of E. coli CCHTP infection in the giant panda.

Histone Methyltransferase G9a Promotes the Development of Renal Cancer through Epigenetic Silencing of Tumor Suppressor Gene SPINK5.

BACKGROUND: Renal cell carcinoma (RCC) accounts for approximately 2-3% of malignant tumors in adults, while clear cell renal cell carcinoma accounts for 70-85% of kidney cancer cases, with an increasing incidence worldwide. G9a is the second histone methyltransferase found in mammals, catalyzing lysine and histone methylation. It regulates gene transcription by catalyzing histone methylation and interacting with transcription factors to alter the tightness of histone-DNA binding. The main purpose of this study is to explore the role and mechanism of G9a in renal cell carcinoma. METHODS: Firstly, we investigated the expression of G9a in 80 clinical tissues and four cell lines. Then, we explored the effect of G9a-specific inhibitor UNC0638 on proliferation, apoptosis, migration, and invasion of two renal cancer cell lines (786-O, SN12C). In order to study the specific mechanism, G9a knocking down renal cancer cell line was constructed by lentivirus. Finally, we identified the downstream target genes of G9a using ChIP experiments and rescue experiments. RESULTS: The results showed that the specific G9a inhibitor UNC0638 significantly inhibited the proliferation, migration, and invasion of kidney cancer in vivo and in vitro; similar results were obtained after knocking down G9a. Meanwhile, we demonstrated that SPINK5 was one of the downstream target genes of G9a through ChIP assay and proved that G9a downregulate the expression of SPINK5 by methylation of H3K9me2. Therefore, targeting G9a might be a new approach to the treatment of kidney cancer. CONCLUSION: G9a was upregulated in renal cancer and could promote the development of renal cancer in vitro and in vivo. Furthermore, we identified SPINK5 as one of the downstream target genes of G9a. Therefore, targeting G9a might be a new treatment for kidney cancer.

Comparison of Intraperitoneal and Intratesticular GYY4137 Therapy for the Treatment of Testicular Ischemia Reperfusion Injury in Rats.

The efficacy of intraperitoneal GYY4137 therapy and intratesticular GYY4137 therapy in an experimental rat model was investigated. Four groups were set up as the sham-operation group, torsion/detorsion (T/D) group, T/D plus intraperitoneal GYY4137 (G-IP) group, and T/D plus intratesticular GYY4137 (G-IT) group. In order to establish a testicular T/D model, the left testis was operated and the rotation reached 720° clockwise which lasted 1 h before reperfusion. The G-IP group accepted 100 µmol/kg of GYY4137 intraperitoneally 30 min after testicular rotation, while the G-IT group was treated with the same dose by intratesticular injection. Six h after detorsion, the testis was collected and subsequently assessed. The T/D group showed significant changes in histology and an enhancement in the level of oxidative stress and apoptosis compared to the sham-operation group. The expression of Caspase-3 and Bax turned out to be strengthened by T/ D and relatively decreased with GYY4137 treatment in both the G-IP and G-IT groups. Moreover, the Bcl-2 expression was inhibited in the T/D group, and promoted by GYY4137 in the G-IP and G-IT groups. GYY4137, moderating these observed changes, displayed a more protective effect with G-IT therapy than G-IP therapy.This study indicated that the efficacy of intratesticular therapy with GYY4137 is better than that of intraperitoneal therapy, which may provide a more valuable approach for testicular torsion therapy.

Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.

The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.

[Effects of wilderness-training Ailuropoda melanoleuca's feeding and artificial harvesting on population structure of Fargesia robusta clone].

From 2003 to 2007, the methods of plot sampling and positioning observation were adopted to investigate the population density, basal diameter, and plant height of Umbrella bamboo (Fargesia robusta) clone in the Wolong Natural Reserve of China. In the meantime, the effects of wilderness-training Ailuropoda melanoleuca's feeding and artificial harvesting on the population regeneration of the clone were studied, and the responses of the population structure (age-, size-, and height-class distribution) to different management modes (A. melanoleuca's feeding, artificial harvesting, control) were approached with the scale- and shape-parameters of Weibull distribution function. The results showed that under the same F. robusta clone population density and the same environmental conditions (P>0.05), A. melanoleuca's feeding and artificial harvesting promoted the clone regeneration. After 3 years natural restoration, the population density of the clone tended to be equal to the control, and came to a steady state (P>0.05). The curves of size- and height-class distribution as well as the scale- and shape-parameters had no significant differences between A. melanoleuca's feeding plot and control plot. The curves of size- and height-class distribution in artificial harvesting plot were in converse "J" shape, and the values of the scale- and shape-parameters were significantly lower than those in the other two plots (P<0.05). The young and adult bamboos in artificial harvesting plot were far poor in shoot quality, and A. melanoleuca rejected to feed with them.