Facile synthesis of Cu N-lauroyl sarcosinate nanozymes with laccase-mimicking activity and identification of toxicity effects for C. elegans.

Nanozyme is a material with enzyme-like catalytic activity, which has been widely used in environmental, antibacterial, and other fields of research. However, there are few reports on the toxicity of nanozymes. In this work, nanozymes co-assembled from sodium N-lauroyl sarcosinate (Ls) and Cu ions possess a Cu(i)-Cu(ii) electron transfer system similar to that of natural laccases. Reaction kinetic studies show that the catalyst follows a typical Michaelis-Menten model. Cu-N-lauroyl sarcosinate nanozyme (Cu-Ls NZ) possess excellent laccase-like activity to oxidize a variety of phenol-containing substrates, such as phenol, 4-iodophenol, and 2,4,5-trichlorophenol. To evaluate the toxicity of the material, the nematode C. elegans was exposed to various concentrations of Cu-Ls NZ. Effects on physiological levels were determined. The results showed that high doses of Cu-Ls NZ increased the amount of reactive oxygen species (ROS), decreased the locomotor activity of nematodes, and inhibited their larval growth.

Detection of ovarian cancer using plasma cell-free DNA methylomes.

BACKGROUND: Ovarian cancer (OC) is a highly lethal gynecologic cancer, and it is hard to diagnose at an early stage. Clinically, there are no ovarian cancer-specific markers for early detection. Here, we demonstrate the use of cell-free DNA (cfDNA) methylomes to detect ovarian cancer, especially the early-stage OC. EXPERIMENTAL DESIGN: Plasma from 74 epithelial ovarian cancer patients, 86 healthy volunteers, and 20 patients with benign pelvic masses was collected. The cfDNA methylomes of these samples were generated by cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq). The differentially methylated regions (DMRs) were identified by the contrasts between tumor and non-tumor groups, and the discrimination performance was evaluated with the iterative training and testing method. RESULTS: The DMRs identified for cfDNA methylomes can well discriminate tumor groups and non-tumor groups (ROC values from 0.86 to 0.98). The late-stage top 300 DMRs are more late-stage-specific and failed to detect early-stage OC. However, the early-stage markers have the potential to discriminate all-stage OCs from non-tumor samples. CONCLUSIONS: This study demonstrates that cfDNA methylomes generated with cfMeDIP-seq could be used to identify OC-specific biomarkers for OC, especially early OC detection. To detect early-stage OC, the biomarkers should be directly identified from early OC plasma samples rather than mix-stage ones. Further exploration of DMRs from a k larger early-stage OC cohort is warranted.

Long-term outcomes of laparoscopic versus open donor nephrectomy for kidney transplantation: a meta-analysis.

Laparoscopic surgery is widely used for living donor nephrectomy and has demonstrated superiority over open surgery by improving several outcomes, such as length of hospital stay and morphine requirements. The purpose of the present study was to compare the long-term outcomes of open donor nephrectomy (ODN) versus laparoscopic donor nephrectomy (LDN) using meta-analytical techniques. The Web of Science, PubMed and Cochrane Library databases were searched, for relevant articles published between 1980 and January 20, 2020. Lists of reference articles retrieved in primary searches were manually screened for potentially eligible studies. Outcome parameters were explored using Review Manager version 5.3. The evaluated outcomes included donor serum creatinine levels, incidence of hypertension or proteinuria at 1 year postoperative, donor health-related quality of life, donation attitude, and graft survival. Thirteen of the 111 articles fulfilled the inclusion criteria. The LDN group demonstrated similar 1 year outcomes compared with ODN with respect to serum creatinine levels (weighted mean difference [WMD] -0.02 mg/dL [95% confidence interval (CI) -0.18-0.13]; P=0.77); hypertension (odds ratio [OR] 1.21 [95% CI 0.48-3.08]; P=0.68); proteinuria (OR 0.28 [95% CI 0.02-3.11]; P=0.30); and donation attitude (OR 4.26 [95% CI 0.06-298.27]; P=0.50). Donor health-related quality of life and recipient graft survival were also not significantly different between the groups analyzed. Thus, the long-term outcomes between LDN and ODN for living donor kidney transplantation are similar.

Correction to: A universal pipeline for mobile mRNA detection and insights into heterografting advantages under chilling stress.

[This corrects the article DOI: 10.1038/s41438-019-0236-1.].

A universal pipeline for mobile mRNA detection and insights into heterografting advantages under chilling stress.

Heterografting has long been used to enhance the chilling tolerance of temperature-sensitive crops, including watermelon, whose mechanism is known to involve bidirectional long-distance mRNA movements. Despite several studies reporting on mobile mRNA (mb-mRNA) profiles in plants, accurate identification of mb-mRNAs is challenging owing to an array of technical problems. Here, we developed a bioinformatical pipeline that took most of the known technical concerns into consideration and is considered to be a universal tool for mb-mRNA detection in heterografts. By applying this pipeline to a commercial watermelon-bottle gourd heterografting system, we detected 130 and 1144 mb-mRNAs upwardly and 167 and 1051 mb-mRNAs downwardly transmitted under normal and chilling-stress conditions, respectively. Quantitative real-time PCR indicated a high accuracy rate (88.2%) of mb-mRNA prediction with our pipeline. We further revealed that the mobility of mRNAs was not associated with their abundance. Functional annotation and classification implied that scions may convey the stress signal to the rootstock, subsequently triggering energy metabolism reprogramming and abscisic acid-mediated stress responses by upward movement of effective mRNAs, ultimately leading to enhanced chilling tolerance. This study provides a universal tool for mb-mRNA detection in plant heterografting systems and novel insights into heterografting advantages under chilling stress.

Generating Homo- and Heterografts Between Watermelon and Bottle Gourd for the Study of Cold-responsive MicroRNAs.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs of about 20 - 24 nt, known to play important roles in plant development and adaptation. There is an accumulating evidence showing that the expressions of certain miRNAs are altered when grafting, an agricultural practice commonly used by farmers to improve crop tolerance to biotic and abiotic stresses. Bottle gourd is an inherently climate-resilient crop compared to many other major cucurbits, including watermelon, rendering it one of the most widely used rootstocks for the latter. The recent advancement of high-throughput sequencing technologies has provided great opportunities to investigate cold-responsive miRNAs and their contributions to heterograft advantages; yet, adequate experimental procedures are a prerequisite for this purpose. Here, we present a detailed protocol for efficiently generating homo- and heterografts between the cold-susceptible watermelon and the cold-tolerant bottle gourd, in addition to methods of tissue sampling, data generation, and data analysis. The presented methods are also useful for other plant-grafting systems, to interrogate miRNA regulations under various environmental stresses, such as heat, drought, and salinity.

PGAP-X: extension on pan-genome analysis pipeline.

BACKGROUND: Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge. RESULT: To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process. CONCLUSION: Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com .

Correlation of MDR1 gene polymorphisms with anesthetic effect of sevoflurane-remifentanil following pediatric tonsillectomy.

BACKGROUND: The motive of this study was to investigate the collaboration between MDR1 gene polymorphisms and anesthetic effects following pediatric tonsillectomy. METHODS: All together 178 children undergoing tonsillectomy with preoperative sevoflurane-remifentanil anesthesia were selected. In order to determine MDR1 gene polymorphisms of 3435C > T, 1236C > T, and 2677G > T/A, polymerase chain reaction-restriction fragment length polymorphism was used. Mean arterial pressure (MAP), diastolic blood pressure (DBP), systolic blood pressure (SBP), and heart rate (HR) at T0 (5 mins after the repose), T1 (0 min after tracheal intubation), T2 (5 mins after the tracheal intubation), T3 (0 min after the tonsillectomy), T4 (0 min after removal of the mouth-gag) and T5 (5 min after the extubation) were observed. The visual analog scale (VAS), the face, legs, activity, cry, and consolability (FLACC) pain assessment, and Ramsay sedation score were recorded after the patients gained consciousness. The adverse reactions were also observed. RESULTS: As compared to the CT + TT genotype of MDR1 1236C > T, the time of induction, respiration recovery, eye-opening, and extubation of children with the CC genotype was found to be shorter (all P <.05); the MAP, SBP, DBP, and HR were significantly reduced at T5 in children that possessed the CC genotype (all P <.05), the VAS at postoperative 1, 2, 4, and 8 hours and Ramsay sedation score were decreased, while the FLACC score increased (all P <.05). It was found that the adverse reaction rate was lower in children bearing the CC genotype (P <.05). CONCLUSION: It could be concluded that anesthetic effect in patients with the MDR1 1236C > T CC genotype was found to be superior to those carrying the CT + TT genotype.

Systematic analysis of intron size and abundance parameters in diverse lineages.

All eukaryotic genomes have genes with introns in variable sizes. As far as spliceosomal introns are concerned, there are at least three basic parameters to stratify introns across diverse eukaryotic taxa: size, number, and sequence context. The number parameter is highly variable in lower eukaryotes, especially among protozoan and fungal species, which ranges from less than 4% to 78% of the genes. Over greater evolutionary time scales, the number parameter undoubtedly increases as observed in higher plants and higher vertebrates, reaching greater than 12.5 exons per gene in average among mammalian genomes. The size parameter is more complex, where multiple modes appear at work. Aside from intronless genes, there are three other types of intron-containing genes: half-sized, minimal, and size-expandable introns. The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes. Among the size-expandable introns, the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals, where the larger introns are filled with transposable elements and appear expansion-flexible, reaching several kilobasepairs (kbp) and even thousands of kbp in size. Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality. In particular, the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.

Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes.

BACKGROUND: Human aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. Due to the high mortality associated with aneuploidy, the pathophysiological mechanisms of aneuploidy syndrome remain largely unknown. Previous studies focused mostly on whether dosage compensation occurs, and the next generation transcriptomics sequencing technology RNA-seq is expected to eventually uncover the mechanisms of gene expression regulation and the related pathological phenotypes in human aneuploidy. RESULTS: Using next generation transcriptomics sequencing technology RNA-seq, we profiled the transcriptomes of four human aneuploid induced pluripotent stem cell (iPSC) lines generated from monosomy × (Turner syndrome), trisomy 8 (Warkany syndrome 2), trisomy 13 (Patau syndrome), and partial trisomy 11:22 (Emanuel syndrome) as well as two umbilical cord matrix iPSC lines as euploid controls to examine how phenotypic abnormalities develop with aberrant karyotype. A total of 466 M (50-bp) reads were obtained from the six iPSC lines, and over 13,000 mRNAs were identified by gene annotation. Global analysis of gene expression profiles and functional analysis of differentially expressed (DE) genes were implemented. Over 5000 DE genes are determined between aneuploidy and euploid iPSCs respectively while 9 KEGG pathways are overlapped enriched in four aneuploidy samples. CONCLUSIONS: Our results demonstrate that the extra or missing chromosome has extensive effects on the whole transcriptome. Functional analysis of differentially expressed genes reveals that the genes most affected in aneuploid individuals are related to central nervous system development and tumorigenesis.

[Cloning and Evolutionary Analysis of Homologous Sequences of CYP86MF Gene in Cruciferae.].

In order to direct the construction of plant germplasms by elucidating the relatives among plants at the level of gene, CYP86MF gene analogues from 11 species of 6 genera in Cuciferae were respectively obtained by PCR strategy using gene specific primers designed from conserved regions of CYP86MF gene reported. Sequence comparisonindicated that the similarities among the genes at nucleotide level were over 80%, and the similarities at amino acid level remained above 70%. The differences between the genes at nucleotide and amino acid level between species were 1.0% ~ 5.7% and 2.6% ~ 7.3% respectively, while those between genera 5.6% ~ 22.5% and 7.3% ~ 31.2%, respectively. Phylogenetic analysis showed that Brassica was closely related to Raphanus, followed by Rorippa Scop, Arabidopsis Heynh, Capsella Medic orderly, most distantly related to Orychophrogmus. It was concluded that CYP86MF gene was not applicable to specie and subspecie taxon but genus taxon because the differences of sequences in nucleotides and amino acids were lower between species than genera.