Progress on phage genomics of Pseudomonas spp.

Pseudomonas spp. are one of the most important ecological flora on the earth, widely distributed in freshwater, soil and other ecological environments. Pseudomonas phages are viruses hosted by Pseudomonas spp., which not only affect the survival and evolution of the hosts, but also play important roles in biomass circulation and energy flow. With the rapid development of genome sequencing technologies, the whole genome sequences of many Pseudomonas phages have been completed. As of July 2020, 247 Pseudomonas phage genomes were deposited in GenBank, accounting for 2.45% of the total 10,069 viral genomes. The genome sizes of Pseudomonas bacteriophages and the genetic contents are different, and the similarity between genomes is low, so the study on Pseudomonas bacteriophage genomes is relatively less. In this review, we summarize the characteristics, genetic diversity, and functional genes of Pseudomonas bacteriophages genomes in order to provide a reference for understanding the antagonistic coevolution of bacteria and phages and the genetic evolution of phages.

Evaluation of the significance of hepatic functional reserve for the operation of liver cancer complicated with cirrhosis.

PURPOSE: To evaluate the significance of hepatic functional reserve for the operation of liver cancer complicated with cirrhosis. METHODS: Fifty-six patients suffering from liver cancer complicated with cirrhosis were divided into three levels, A, B and C, according to Child-Pugh grading system. Based on indocyanine green retention rate at 15 min (ICGR15) value, patients were divided into three intervals, ≤15%, 15-25% and ≥25%. According to the existence of complications, patients were divided into the complication group and the no complication group. RESULTS: Child-Pugh grading included 50 cases of level A, 45 cases of B and 29 cases of C. ICGR15 value included 47 cases of ≤15% interval, 47 cases of 15-25% and 30 cases of ≥25%. As the IGCR15 value increased, the levels of all indicators were obviously increased. Among the 124 patients, 35 cases (28.23%) suffered complications The median follow-up time was 25.0 months. The survival rate of the complication group was 60.00% (21 cases), significantly lower than that of the no complication group (84.27%). Child-Pugh grading of the complication group included 4 cases of level A, 12 cases of B and 19 cases of C. ICGR15 value included 15 cases of 15~25% interval and 20 cases of ≥25%. CONCLUSION: Child-Pugh grading and ICGR15 value can both reflect hepatic functional reserve and are of great clinical significance for complication and survival. There is a fairly good relevance between ICGR15 and levels of AFP, ALT and indicators of liver fibrosis.

Updated meta-analysis on HER2 polymorphisms and risk of breast cancer: evidence from 32 studies.

BACKGROUND: Several studies have been performed to investigate the association of the HER2 Ile655Val polymorphism and breast cancer risk. However, the results were inconsistent. To understand the precise relationship, a meta-analysis was here conducted. MATERIALS AND METHODS: A search of PubMed conducted to investigate links between the HER2 Ile655Val polymorphism and breast cancer, identified a total of 32 studies, of which 29, including 14,926 cases and 15,768 controls, with odds ratios (ORs) with 95% confidence intervals were used to assess any association. RESULTS: In the overall analysis, the HER2 Ile655Val polymorphism was associated with breast cancer in an additive genetic model (OR=1.136, 95% CI 1.043-1.239, p=0.004) and in a dominant genetic (OR=1.118, 95% CI 1.020-1.227, p=0.018), while no association was found in a recessive genetic model. On subgroup analysis, an association with breast cancer was noted in the additive genetic model (OR=1.111, 95% CI: 1.004-1.230, p=0.042) for the Caucasian subgroup. No significant associations were observed in Asians and Africans in any of the genetic models. CONCLUSIONS: In summary, our meta-analysis findings suggest that the HER2 Ile655Val polymorphism is marginally associated with breast cancer susceptibility in worldwide populations with additive and dominant models, but not a recessive model.

Association of DR4 (TRAIL-R1) polymorphisms with cancer risk in Caucasians: an updated meta-analysis.

Death receptor 4 (TRAIL-R1 or DR4) polymorphisms have been associated with cancer risk, but findings have been inconsistent. To estimate the relationship in detail, a meta-analysis was here performed. A search of PubMed was conducted to investigate the association between DR4 C626G, A683C and A1322G polymorphisms and cancer risk, using odds ratios (ORs) with 95% confidence intervals. The results suggested that DR4 C626G and A683C polymorphisms were indeed associated with cancer risk (for C626G, dominant model, OR 0.991, 95%CI 0.866-1.133, p=0.015; for A683C, additive model, OR=1.140, 95%CI: 0.948-1.370, p=0.028; dominant model, OR=1.156, 95%CI: 0.950-1.406, p=0.080) in the Caucasian subgroup. However, the association was not significant between DR4 polymorphism A1322G with cancer risk in Caucasians (For A1322G, additive model: OR 1.085, 95%CI 0.931-1.289, p=0.217; dominant model: OR 1.379, 95%CI 0.934-2.035, p=0.311; recessive model: OR 1.026, 95%CI 0.831-1.268 p=0.429.). In summary, our finding suggests that DR4 polymorphism C626G and A683 rather than A1322G are associated with cancer risk in Caucasians.

Laceyella sediminis sp. nov., a thermophilic bacterium isolated from a hot spring.

A thermophilic bacterium, designated strain RHA1(T), was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China, and was characterized by using a polyphasic approach. Based on its phenotypic and phylogenetic characteristics, strain RHA1(T) was affiliated to the genus Laceyella. The strain formed white aerial and yellow-white substrate mycelia, bearing single endospores on short sporophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Whole-cell hydrolysates contained ribose and glucose. The major fatty acids were iso-C(15:0) (62.39%) and anteiso-C(15:0) (17.55%)(.) The predominant menaquinone was MK-9. The G+C content of the genomic DNA of strain RHA1(T) was 47.9 mol%. Based on DNA-DNA hybridization data, chemotaxonomic characteristics and differential physiological properties, strain RHA1(T) is considered to represent a novel species of the genus Laceyella, for which the name Laceyella sediminis sp. nov. is proposed; the type strain is RHA1(T) (=DSM 45263(T)=CCTCC AA 208058(T)).

[Construction of promoter probe vector for a cold-adapted bacterium, Acinetobacter sp. DWC6].

In order to build a protein expression system in a cold-adapted bacterium Acinetobacter sp. DWC6, a promoter probe vector was constructed based on the plasmid pBR322. A fragment containing the promoter of the beta-lactamase gene (the ampicillin resistance gene) in pBR322 was eliminated and replaced by a fragment comprizing a kanamycin resistance gene amplified from pJRD215. DNA fragment harboring in the Acinetobacter species specific ori was also inserted into the plasmid pBR322 to construct a promoter probe vector named pBAP1, which could replicate both in E. coli and in Acinetobacter sp. DWC6. The promoter selection library was constructed by randomly inserting genomic DNA fragment of Acinetobacter sp. DWC6 at upstream of reported gene, and target promoters were screened from genomic library on ampicillin selection plates. The function of pBAP1 and isolated promoters were determined by detection of the ampicillin sensitivity and the expression level of beta-lactamase in the host cell.

Construction of a low-temperature protein expression system using a cold-adapted bacterium, Shewanella sp. strain Ac10, as the host.

A recombinant protein expression system working at low temperatures is expected to be useful for the production of thermolabile proteins. We constructed a low-temperature expression system using an Antarctic cold-adapted bacterium, Shewanella sp. strain Ac10, as the host. We evaluated the promoters for proteins abundantly produced at 4 degrees C in this bacterium to express foreign proteins. We used 27 promoters and a broad-host-range vector, pJRD215, to produce beta-lactamase in Shewanella sp. strain Ac10. The maximum yield was obtained when the promoter for putative alkyl hydroperoxide reductase (AhpC) was used and the recombinant cells were grown to late stationary phase. The yield was 91 mg/liter of culture at 4 degrees C and 139 mg/liter of culture at 18 degrees C. We used this system to produce putative peptidases, PepF, LAP, and PepQ, and a putative glucosidase, BglA, from a psychrophilic bacterium, Desulfotalea psychrophila DSM12343. We obtained 48, 7.1, 28, and 5.4 mg/liter of culture of these proteins, respectively, in a soluble fraction. The amounts of PepF and PepQ produced by this system were greater than those produced by the Escherichia coli T7 promoter system.