LIVIVO - Search results -

Search results

Result 1 - 10 of total 14

Search options

Article: Laparoscopic versus open pancreaticoduodenectomy for pancreatic and periampullary tumor: A meta-analysis of randomized controlled trials and non-randomized comparative studies.

Yan, Yong / Hua, Yinggang / Chang, Cheng / Zhu, Xuanjin / Sha, Yanhua / Wang, Bailin

2023 Volume 12, Page(s) 1093395

Abstract: Objective: This meta-analysis compares the perioperative outcomes of laparoscopic pancreaticoduodenectomy (LPD) to those of open pancreaticoduodenectomy (OPD) for pancreatic and periampullary tumors.: Background: LPD has been increasingly applied in ... ...

Abstract	Objective: This meta-analysis compares the perioperative outcomes of laparoscopic pancreaticoduodenectomy (LPD) to those of open pancreaticoduodenectomy (OPD) for pancreatic and periampullary tumors. Background: LPD has been increasingly applied in the treatment of pancreatic and periampullary tumors. However, the perioperative outcomes of LPD versus OPD are still controversial. Methods: PubMed, Web of Science, EMBASE, and the Cochrane Library were searched to identify randomized controlled trials (RCTs) and non-randomized comparative trials (NRCTs) comparing LPD versus OPD for pancreatic and periampullary tumors. The main outcomes were mortality, morbidity, serious complications, and hospital stay. The secondary outcomes were operative time, blood loss, transfusion, postoperative pancreatic fistula (POPF), postpancreatectomy hemorrhage (PPH), bile leak (BL), delayed gastric emptying (DGE), lymph nodes harvested, R0 resection, reoperation, and readmission. RCTs were evaluated by the Cochrane risk-of-bias tool. NRCTs were assessed using a modified tool from the Methodological Index for Non-randomized Studies. Data were pooled as odds ratio (OR) or mean difference (MD). This study was registered at PROSPERO (CRD42022338832). Results: Four RCTs and 35 NRCTs concerning a total of 40,230 patients (4,262 LPD and 35,968 OPD) were included. Meta-analyses showed no significant differences in mortality (OR 0.91, Conclusions: LPD is associated with non-inferior short-term surgical outcomes and oncologic adequacy compared to OPD when performed by experienced surgeons at large centers. LPD may result in reduced overall morbidity, blood loss, transfusion, and DGE, but longer operative time. Further RCTs should address the potential advantages of LPD over OPD. Systematic review registration: PROSPERO, identifier CRD42022338832.
Language	English
Publishing date	2023-01-25
Publishing country	Switzerland
Document type	Systematic Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2022.1093395
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

Cheng, Xuanjin / Yan, Junran / Liu, Yongxing / Wang, Jiahe / Taubert, Stefan

Nucleic acids research

2021 Volume 49, Issue W1, Page(s) W207–W215

Abstract: Transcriptome profiling is essential for gene regulation studies in development and disease. Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, ...

Abstract	Transcriptome profiling is essential for gene regulation studies in development and disease. Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, inefficient in leveraging up-to-date and species-specific information, and limited in their visualization options. Additionally, there is no systematic way to explore data stored in the largest transcriptome repository, NCBI GEO. To fill these gaps, we have developed eVITTA (easy Visualization and Inference Toolbox for Transcriptome Analysis; https://tau.cmmt.ubc.ca/eVITTA/). eVITTA provides modules for analysis and exploration of studies published in NCBI GEO (easyGEO), detailed molecular- and systems-level functional profiling (easyGSEA), and customizable comparisons among experimental groups (easyVizR). We tested eVITTA on transcriptomes of SARS-CoV-2 infected human nasopharyngeal swab samples, and identified a downregulation of olfactory signal transducers, in line with the clinical presentation of anosmia in COVID-19 patients. We also analyzed transcriptomes of Caenorhabditis elegans worms with disrupted S-adenosylmethionine metabolism, confirming activation of innate immune responses and feedback induction of one-carbon cycle genes. Collectively, eVITTA streamlines complex computational workflows into an accessible interface, thus filling the gap of an end-to-end platform capable of capturing both broad and granular changes in human and model organism transcriptomes.
MeSH term(s)	Animals ; COVID-19/genetics ; COVID-19/virology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Data Visualization ; Databases, Genetic ; Gene Expression Profiling/methods ; Humans ; Immunity, Innate ; Internet ; Nasopharynx/virology ; S-Adenosylmethionine/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/pathogenicity ; Species Specificity ; Transcriptome/genetics ; Workflow
Chemical Substances	S-Adenosylmethionine (7LP2MPO46S)
Language	English
Publishing date	2021-05-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab366
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1067: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Nuclear hormone receptor NHR-49 acts in parallel with HIF-1 to promote hypoxia adaptation in

Doering, Kelsie R S / Cheng, Xuanjin / Milburn, Luke / Ratnappan, Ramesh / Ghazi, Arjumand / Miller, Dana L / Taubert, Stefan

eLife

2022 Volume 11

Abstract: The response to insufficient oxygen (hypoxia) is orchestrated by the conserved hypoxia-inducible factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel with HIF to mediate the physiological hypoxia response. Here, we ... ...

Abstract	The response to insufficient oxygen (hypoxia) is orchestrated by the conserved hypoxia-inducible factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel with HIF to mediate the physiological hypoxia response. Here, we describe a hypoxia response pathway controlled by
MeSH term(s)	Animals ; Caenorhabditis elegans/physiology ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Hypoxia/genetics ; Hypoxia-Inducible Factor 1/metabolism ; Mammals/metabolism ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; HIF-1 protein, C elegans ; Hypoxia-Inducible Factor 1 ; NHR-49 protein, C elegans ; Nhr-67 protein, C elegans ; Receptors, Cytoplasmic and Nuclear ; Transcription Factors
Language	English
Publishing date	2022-03-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.67911
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Nuclear hormone receptor NHR-49 acts in parallel with HIF-1 to promote hypoxia adaptation in Caenorhabditis elegans

Kelsie RS Doering / Xuanjin Cheng / Luke Milburn / Ramesh Ratnappan / Arjumand Ghazi / Dana L Miller / Stefan Taubert

eLife, Vol

2022 Volume 11

Abstract	The response to insufficient oxygen (hypoxia) is orchestrated by the conserved hypoxia-inducible factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel with HIF to mediate the physiological hypoxia response. Here, we describe a hypoxia response pathway controlled by Caenorhabditis elegans nuclear hormone receptor NHR-49, an orthologue of mammalian peroxisome proliferator-activated receptor alpha (PPARα). We show that nhr-49 is required for animal survival in hypoxia and is synthetic lethal with hif-1 in this context, demonstrating that these factors act in parallel. RNA-seq analysis shows that in hypoxia nhr-49 regulates a set of genes that are hif-1-independent, including autophagy genes that promote hypoxia survival. We further show that nuclear hormone receptor nhr-67 is a negative regulator and homeodomain-interacting protein kinase hpk-1 is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel with the well-known HIF-mediated hypoxia response.
Keywords	hypoxia ; gene expression ; transcription factors ; nuclear receptor ; HIF ; autophagy ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines.

Cheng, Xuanjin / Liu, Yongxing / Wang, Jiahe / Chen, Yujie / Robertson, Andrew Gordon / Zhang, Xuekui / Jones, Steven J M / Taubert, Stefan

Briefings in bioinformatics

2022 Volume 23, Issue 3

Abstract: Survival analysis is a technique for identifying prognostic biomarkers and genetic vulnerabilities in cancer studies. Large-scale consortium-based projects have profiled >11 000 adult and >4000 pediatric tumor cases with clinical outcomes and multiomics ... ...

Abstract	Survival analysis is a technique for identifying prognostic biomarkers and genetic vulnerabilities in cancer studies. Large-scale consortium-based projects have profiled >11 000 adult and >4000 pediatric tumor cases with clinical outcomes and multiomics approaches. This provides a resource for investigating molecular-level cancer etiologies using clinical correlations. Although cancers often arise from multiple genetic vulnerabilities and have deregulated gene sets (GSs), existing survival analysis protocols can report only on individual genes. Additionally, there is no systematic method to connect clinical outcomes with experimental (cell line) data. To address these gaps, we developed cSurvival (https://tau.cmmt.ubc.ca/cSurvival). cSurvival provides a user-adjustable analytical pipeline with a curated, integrated database and offers three main advances: (i) joint analysis with two genomic predictors to identify interacting biomarkers, including new algorithms to identify optimal cutoffs for two continuous predictors; (ii) survival analysis not only at the gene, but also the GS level; and (iii) integration of clinical and experimental cell line studies to generate synergistic biological insights. To demonstrate these advances, we report three case studies. We confirmed findings of autophagy-dependent survival in colorectal cancers and of synergistic negative effects between high expression of SLC7A11 and SLC2A1 on outcomes in several cancers. We further used cSurvival to identify high expression of the Nrf2-antioxidant response element pathway as a main indicator for lung cancer prognosis and for cellular resistance to oxidative stress-inducing drugs. Altogether, these analyses demonstrate cSurvival's ability to support biomarker prognosis and interaction analysis via gene- and GS-level approaches and to integrate clinical and experimental biomedical studies.
MeSH term(s)	Adult ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Line ; Child ; Gene Expression Regulation, Neoplastic ; Humans ; Lung Neoplasms/genetics ; Survival Analysis
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac090
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Abnormal brain activity in lumbar disc herniation patients with chronic pain is associated with their clinical symptoms.

Tang, Cheng / Guo, Guangxin / Fang, Sitong / Yao, Chongjie / Zhu, Bowen / Kong, Lingjun / Pan, Xuanjin / Li, Xinrong / He, Weibin / Wu, Zhiwei / Fang, Min

Frontiers in neuroscience

2023 Volume 17, Page(s) 1206604

Abstract: Introduction: Lumbar disc herniation, a chronic degenerative disease, is one of the major contributors to chronic low back pain and disability. Although many studies have been conducted in the past on brain function in chronic low back pain, most of ... ...

Abstract	Introduction: Lumbar disc herniation, a chronic degenerative disease, is one of the major contributors to chronic low back pain and disability. Although many studies have been conducted in the past on brain function in chronic low back pain, most of these studies did not classify chronic low back pain (cLBP) patients according to their etiology. The lack of etiologic classification may lead to inconsistencies between findings, and the correlation between differences in brain activation and clinical symptoms in patients with cLBP was less studied in the past. Methods: In this study, 36 lumbar disc herniation patients with chronic low back pain (LDHCP) and 36 healthy controls (HCs) were included to study brain activity abnormalities in LDHCP. Visual analogue scale (VAS), oswestry disability index (ODI), self-rating anxiety scale (SAS), self-rating depression scale (SDS) were used to assess clinical symptoms. Results: The results showed that LDHCP patients exhibited abnormally increased and diminished activation of brain regions compared to HCs. Correlation analysis showed that the amplitude of low frequency fluctuations (ALFF) in the left middle frontal gyrus is negatively correlated with SAS and VAS, while the right superior temporal gyrus is positively correlated with SAS and VAS, the dorsolateral left superior frontal gyrus and the right middle frontal gyrus are negatively correlated with VAS and SAS, respectively. Conclusion: LDHCP patients have brain regions with abnormally increased and abnormally decreased activation compared to healthy controls. Furthermore, some of the abnormally activated brain regions were correlated with clinical pain or emotional symptoms.
Language	English
Publishing date	2023-07-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/fnins.2023.1206604
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: A "developmental hourglass" in fungi.

Cheng, Xuanjin / Hui, Jerome Ho Lam / Lee, Yung Yung / Wan Law, Patrick Tik / Kwan, Hoi Shan

Molecular biology and evolution

2015 Volume 32, Issue 6, Page(s) 1556–1566

Abstract: The "developmental hourglass" concept suggests that intermediate developmental stages are most resistant to evolutionary changes and that differences between species arise through divergence later in development. This high conservation during ... ...

Abstract	The "developmental hourglass" concept suggests that intermediate developmental stages are most resistant to evolutionary changes and that differences between species arise through divergence later in development. This high conservation during middevelopment is illustrated by the "waist" of the hourglass and it represents a low probability of evolutionary change. Earlier molecular surveys both on animals and on plants have shown that the genes expressed at the waist stage are more ancient and more conserved in their expression. The existence of such a developmental hourglass has not been explored in fungi, another eukaryotic kingdom. In this study, we generated a series of transcriptomic data covering the entire lifecycle of a model mushroom-forming fungus, Coprinopsis cinerea, and we observed a molecular hourglass over its development. The "young fruiting body" is the stage that expresses the evolutionarily oldest (lowest transcriptome age index) transcriptome and gives the strongest signal of purifying selection (lowest transcriptome divergence index). We also demonstrated that all three kingdoms-animals, plants, and fungi-display high expression levels of genes in "information storage and processing" at the waist stages, whereas the genes in "metabolism" become more highly expressed later. Besides, the three kingdoms all show underrepresented "signal transduction mechanisms" at the waist stages. The synchronic existence of a molecular "hourglass" across the three kingdoms reveals a mutual strategy for eukaryotes to incorporate evolutionary innovations.
MeSH term(s)	Agaricales/genetics ; Evolution, Molecular ; Fruiting Bodies, Fungal/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Microarray Analysis ; Models, Genetic ; RNA, Fungal/genetics ; Transcriptome
Chemical Substances	RNA, Fungal
Language	English
Publishing date	2015-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msv047
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2137: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea.

Amy Yuet Ting Lau / Xuanjin Cheng / Chi Keung Cheng / Wenyan Nong / Man Kit Cheung / Raymond Hon-Fu Chan / Jerome Ho Lam Hui / Hoi Shan Kwan

PLoS ONE, Vol 13, Iss 9, p e

2018 Volume 0198234

Abstract: Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential ...

Abstract	Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China.

Xiao, Yang / Cheng, Xuanjin / Liu, Jun / Li, Chuang / Nong, Wenyan / Bian, Yinbing / Cheung, Man Kit / Kwan, Hoi Shan

Scientific reports

2016 Volume 6, Page(s) 36789

Abstract: The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake ... ...

Abstract	The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.
MeSH term(s)	Adaptation, Physiological ; China ; DNA, Fungal/genetics ; Evolution, Molecular ; Fruiting Bodies, Fungal/genetics ; Fruiting Bodies, Fungal/growth & development ; Genome, Fungal ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA ; Shiitake Mushrooms/genetics ; Shiitake Mushrooms/growth & development ; Stress, Physiological
Chemical Substances	DNA, Fungal
Language	English
Publishing date	2016-11-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep36789
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea.

Lau, Amy Yuet Ting / Cheng, Xuanjin / Cheng, Chi Keung / Nong, Wenyan / Cheung, Man Kit / Chan, Raymond Hon-Fu / Hui, Jerome Ho Lam / Kwan, Hoi Shan

PloS one

2018 Volume 13, Issue 9, Page(s) e0198234

Abstract	Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.
MeSH term(s)	Base Sequence ; Coprinus/genetics ; Fruiting Bodies, Fungal/genetics ; Fungal Proteins/genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Genomics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/genetics ; Phylogeny ; RNA, Fungal/genetics ; Transcriptome
Chemical Substances	Fungal Proteins ; MicroRNAs ; RNA, Fungal
Language	English
Publishing date	2018-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0198234
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED