A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors.

Poly (ADP-ribose) polymerase (PARP) inhibitors are one of the most exciting classes of targeted therapy agents for cancers with homologous recombination (HR) deficiency. However, many patients without apparent HR defects also respond well to PARP inhibitors/cisplatin. The biomarker responsible for this mechanism remains unclear. Here, we identified a set of ribosomal genes that predict response to PARP inhibitors/cisplatin in HR-proficient patients. PARP inhibitor/cisplatin selectively eliminates cells with high expression of the eight genes in the identified panel via DNA damage (ATM) signaling-induced pro-apoptotic ribosomal stress, which along with ATM signaling-induced pro-survival HR repair constitutes a new model to balance the cell fate in response to DNA damage. Therefore, the combined examination of the gene panel along with HR status would allow for more precise predictions of clinical response to PARP inhibitor/cisplatin. The gene panel as an independent biomarker was validated by multiple published clinical datasets, as well as by an ovarian cancer organoids library we established. More importantly, its predictive value was further verified in a cohort of PARP inhibitor-treated ovarian cancer patients with both RNA-seq and WGS data. Furthermore, we identified several marketed drugs capable of upregulating the expression of the genes in the panel without causing HR deficiency in PARP inhibitor/cisplatin-resistant cell lines. These drugs enhance PARP inhibitor/cisplatin sensitivity in both intrinsically resistant organoids and cell lines with acquired resistance. Together, our study identifies a marker gene panel for HR-proficient patients and reveals a broader application of PARP inhibitor/cisplatin in cancer therapy.

Patient satisfaction with nurses' care is positively related to the nurse-patient relationship in Chinese hospitals: A multicentre study.

Background: The nurse-patient relationship and nursing care satisfaction are important factors that represent whether patients experience the care they expect from nurses. However, research is lacking on the relationship between nursing staff and patients, and the correlation between nursing care satisfaction and relationship care in China. Therefore, this study aimed to explore the correlation between the nurse-patient relationship and patients' satisfaction with nursing care, to form a basis for corresponding intervention measures. Methods: A total of 29,108 patients from 107 hospitals in 30 provinces/municipalities in China completed a general information questionnaire, the Nursing Care Satisfaction Scale, and Relational Care Scale. Results: The average nurse-patient relational care scale score was 4.38 ± 0.57, and the average patients' satisfaction with nursing care scale score was 5.40 ± 0.86. Nursing care satisfaction score was significantly related to differences among patients in different age, gender, marital status, education level, occupation, residence, family per capita monthly income, type of medical insurance, medical department, and regional patient characteristics. The correlation analysis showed that the total nurse-patient relational care score and its three dimensions of caring, trust, and professional ethics correlated positively with nursing care satisfaction scores. The multiple linear regression analysis showed that patients' age, marital status, region, department, income, type of medical insurance and the caring, trust, and professional ethics dimensions of relational care predicted nursing care satisfaction. Conclusion: Enhancing nurse-patient relational care improves nursing care satisfaction, reduces nurse-patient disputes, promotes early rehabilitation of patients, and ensures patient safety.

Production of a Functional Frozen Yogurt Fortified with Bifidobacterium spp.

Frozen dairy products have characteristics of both yogurt and ice cream and could be the persuasive carriers of probiotics. Functions of the frozen yogurt containing viable bifidobacterial cells are recognized and favored by the people of all ages. We developed a kind of yogurt supplemented by Bifidobacterium species. Firstly, five strains of Bifidobacterium spp. (Bifidobacterium bifidum ATCC 11547, Bifidobacterium longum ATCC 11549, Bifidobacterium infantis ATCC 11551, Bifidobacterium adolescentis ATCC 11550, and Bifidobacterium breve ATCC 11548) were evaluated based on the feasibility criteria of probiotics, comprising acid production, bile tolerance, and adhesion to epithelial cells. Formerly, we combined the optimum strains with yogurt culture (Lactobacillus delbrueckii subsp. bulgaricus EMCC 11102 and Streptococcus salivarius subsp. thermophilus EMCC 11044) for producing frozen yogurt. Finally, physiochemical properties and sensory evaluation of the frozen yogurt were investigated during storage of 60 days at -18°C. Results directed that Bifidobacterium adolescentis ATCC 11550 and Bifidobacterium infantis ATCC 11551 could be utilized with yogurt culture for producing frozen yogurt. Moreover, the frozen yogurt fermented by two bifidobacterial strains and yogurt culture gained the high evaluation in the physiochemical properties and sensory evaluation. In summary, our results revealed that there was no significant difference between frozen yogurt fermented by Bifidobacterium spp. and yogurt culture and that fermented by yogurt culture only.

A novel protein, Rsf1/Pxd1, is critical for the single-strand annealing pathway of double-strand break repair in Schizosaccharomyces pombe.

The process of single-strand annealing (SSA) repairs DNA double-strand breaks that are flanked by direct repeat sequences through the coordinated actions of a series of proteins implicated in recombination, mismatch repair and nucleotide excision repair (NER). Many of the molecular and mechanistic insights gained in SSA repair have principally come from studies in the budding yeast Saccharomyces cerevisiae. However, there is little molecular understanding of the SSA pathway in the fission yeast Schizosaccharomyces pombe. To further our understanding of this important process, we established a new chromosome-based SSA assay in fission yeast. Our genetic analyses showed that, although many homologous components participate in SSA repair in these species indicating that some evolutionary conservation, Saw1 and Slx4 are not principal agents in the SSA repair pathway in fission yeast. This is in marked contrast to the function of Saw1 and Slx4 in budding yeast. Additionally, a novel genus-specific protein, Rsf1/Pxd1, physically interacts with Rad16, Swi10 and Saw1 in vitro and in vivo. We find that Rsf1/Pxd1 is not required for NER and demonstrate that, in fission yeast, Rsf1/Pxd1, but not Saw1, plays a critical role in SSA recombination.

Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4.

The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize.

BACKGROUND: Bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as Arabidopsis and rice. Little is known about bidirectional gene pairs in maize, which has a large genome and is one of the most important grain crops. RESULTS: We conducted a genome-wide search in maize using genome sequencing results from the inbred line B73. In total, 1696 bidirectional transcript pairs were identified using a modified search model. We functionally characterized the promoter activity of the intergenic regions of most of the bidirectional transcript pairs that were expressed in embryos using a maize embryo transient expression system. A comparative study of bidirectional gene pairs performed for three monocot (Zea mays, Sorghum bicolor and Oryza sativa) and two dicot (Arabidopsis thaliana and Glycine max) plant genomes showed that bidirectional gene pairs were abundant in the five plant species. Orthologous bidirectional gene pairs were clearly distinguishable between the monocot and dicot species although the total numbers of orthologous bidirectional genes were similar. Analysis of the gene pairs using the Blast2GO software suite showed that the molecular functions (MF), cellular components (CC), and biological processes (BP) associated with the bidirectional transcripts were similar among the five plant species. CONCLUSIONS: The evolutionary analysis of the function and structure of orthologous bidirectional gene pairs in various plant species revealed a potential pathway of their origin, which may be required for the evolution of a new species.

Family-wide survey of miR169s and NF-YAs and their expression profiles response to abiotic stress in maize roots.

Previous studies have identified miR169/NF-YA modules are important regulators of plant development and stress responses. Currently, reported genome sequence data offers an opportunity for global characterization of miR169 and NF-YA genes, which may provide insights into the molecular mechanisms of the miR169/NF-YA modules in maize. In our study, fourteen NF-YA transcription factors with conserved domains were identified based on maize genome loci. The miR169 gene family has 18 members that generate 10 mature products, and 8 of these mature miR169 members could target 7 of 14 ZmNF-YA genes in maize. The seven ZmNF-YA proteins were localized to the nucleus while lacked transcriptional activity. We investigated the expression patterns of the zma-miR169 members and their targeted ZmNF-YA genes in maize roots treated by drought stress (polyethylene glycol, PEG), hormone stress (abscisic acid, ABA), and salt stress (NaCl). The zma-miR169 family members were downregulated in short term (0 ∼ 48 h) and generally upregulated over the long term (15 days) in response to the three abiotic stress conditions. Most of the targeted ZmNF-YA genes exhibited a reverse correlation with zma-miR169 gene expression over both the short term and long term. Maize root elongation was promoted by PEG and ABA but repressed by NaCl over the long term. Apparently, ZmNF-YA14 expression perfectly matched the zma-miR169 expression and corresponded to root growth reversely.

Construction of a genomewide RNAi mutant library in rice.

Long hairpin RNA (hpRNA) transgenes are a powerful tool for gene function studies in plants, but a genomewide RNAi mutant library using hpRNA transgenes has not been reported for plants. Here, we report the construction of a hpRNA library for the genomewide identification of gene function in rice using an improved rolling circle amplification-mediated hpRNA (RMHR) method. Transformation of rice with the library resulted in thousands of transgenic lines containing hpRNAs targeting genes of various function. The target mRNA was down-regulated in the hpRNA lines, and this was correlated with the accumulation of siRNAs corresponding to the double-stranded arms of the hpRNA. Multiple members of a gene family were simultaneously silenced by hpRNAs derived from a single member, but the degree of such cross-silencing depended on the level of sequence homology between the members as well as the abundance of matching siRNAs. The silencing of key genes tended to cause a severe phenotype, but these transgenic lines usually survived in the field long enough for phenotypic and molecular analyses to be conducted. Deep sequencing analysis of small RNAs showed that the hpRNA-derived siRNAs were characteristic of Argonaute-binding small RNAs. Our results indicate that RNAi mutant library is a high-efficient approach for genomewide gene identification in plants.