scholarly journals Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection

2019 ◽  
Author(s):  
Rui Guo ◽  
Huazhi Chen ◽  
Yu Du ◽  
Dingding Zhou ◽  
Sihai Geng ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Expression Pattern ◽  
Structural Features ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Form Complex ◽  
Apis Mellifera Ligustica ◽  
Wide Range ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proved to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression pattern and potential role of honeybee lncRNAs response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had low sequence similarities with other known lncRNAs in other species; however, their structural features were similar with counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7 day post inoculation (dpi) and 10 dpi compared with control midguts. 12 differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs Am7T and Am10CK vs Am10T comparison groups, while the numbers of unique ones were 99 and 134, respectively. Functional annotation and pathway analysis showed the DElncRNAs may regulate the expression of neighboring genes by acting in cis. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the result demonstrated that part of DElncRNAs were likely to participate in regulating the material and energy metabolism as well as cellular and humoral immune during host responses to N. ceranae invasion. Finally, the expression pattern of 10 DElncRNAs was validated using RT-qPCR, confirming the reliability of our sequencing data. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding host-pathogen interaction during microsporidiosis of honeybee.

scholarly journals Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection

Insects ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 245 ◽  
Author(s):  
Dafu Chen ◽  
Huazhi Chen ◽  
Yu Du ◽  
Dingding Zhou ◽  
Sihai Geng ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Structural Features ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Form Complex ◽  
Apis Mellifera Ligustica ◽  
Wide Range ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.

scholarly journals Whole transcriptome data of uninfected and Nosema ceranae-infected midguts of eastern honeybee workers

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Dingding Zhou ◽  
Yu Du ◽  
Cuiling Xiong ◽  
Yanzhen Zheng ◽  
...  
Keyword(s):  
Apis Cerana ◽  
Gc Content ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
List Type ◽  
Valuable Resource ◽  
Fungal Parasite ◽  
Differential Expression Pattern ◽  
Non Coding Rnas ◽  
Whole Transcriptome

ABSTRACTApis cerana cerana is a subspecies of eastern honeybee, Apis cerana. Nosema ceranae is a widespread fungal parasite of honeybee, causing heavy losses for beekeeping industry all over the world. In this article, total RNA of normal midguts (AcCK1, AcCK2) and N. ceranae-infected midguts of A. c. cerana workers at 7 d and 10 d post inoculation (AcT1, AcT2) were respectively isolated followed by strand-specific cDNA library construction and next-generation RNA sequencing. In tolal, 56270223688, 44860946964, 78991623806, and 92712308296 raw reads were derived from AcCK1, AcCK2, AcT1 and AcT2, respectively. Following strict quality control, 54495191388, 43570608753, 76708161525, and 89467858351 clean reads were obtained, with Q30 value of 95.80%, 95.99%, 96.07% and 96.04%, and GC content of 44.20%, 43.44%, 44.83% and 43.63%, respectively. The raw data were submitted to the NCBI Sequence Read Archive database and connected to BioProject PRJNA562784. These data offers a valuable resource for deep investigation of mechanisms underlying eastern honeybee responding to N. ceranae infection and host-fungal parasite interaction during microsporidiosis.Value of the DataCurrent dataset offers a valuable resource for exploring mRNAs, lncRNAs and circRNAs involved in response of A. c. cerana worker to N. ceranae infection.The accessible data can be used to investigate differential expression pattern and regulatory network of non-coding RNAs in A. c. cerana workers’ midguts responding to N. ceranae challenge.This data will enable a better understanding of the molecular mechanism regulating eastern honeybee-N. ceranae interaction.

scholarly journals Nanopore-based genome-wide DNA methylation sequencing data of Nosema ceranae-inoculated and un-inoculated eastern honeybee workers' midguts

2021 ◽  
Author(s):  
Jun Ke Yu ◽  
Da Fu Chen ◽  
Rui Guo
Keyword(s):  
Dna Methylation ◽  
Host Response ◽  
Reference Genome ◽  
Apis Cerana ◽  
Vital Role ◽  
Nosema Ceranae ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Average Quality ◽  
Genome Wide

Apis cerana cerana is an excellent subspecies of Apis cerana, playing a vital role in pollination for wild flowers and crops as well as ecological balance. Nosema ceranae, an emergent fungal parasite infecting various bee species, originates from eastern honeybee. In this article, midguts of N. ceranae-inoculated A. c. cerana workers at 7 days post inoculation (dpi) and 10 dpi (AcT1 and AcT2) and un-inoculated workers' midguts (AcCK1, AcCK2) were subjected to Nanopore-based genome-wide DNA methylation sequencing. Totally, 1773258, 2151476, 1927874 and 2109961 clean reads were generated from AcCK1, AcCK2, AcT1, and AcT2 groups, with the N50 lengths of 7548, 7936, 7678, and 7291 and the average quality value of 8.97, 8.95, 9.24, and 8.98, respectively. Among these, 93.85%, 94.49%, 88.69%, and 81.27% clean reads could be mapped to the reference genome of A. c. cerana. In the aforementioned four groups, 2149685, 2614513, 1637018 and 2726985 CHG sites were identified; the numbers of CHH sites were 9581990, 11801082, 7178559, and 12342423, whereas those of CpG sites were 14325356, 15703508, 14856284 and 13956849, respectively. Additionally, there were 36114, 118867, 30249, and 82984 6mA methylation sites respectively discovered. These data can be used for identifying differential 5mC methylation and 6mA methylation engaged in response of eastern honeybee workers to N. ceranae infestation, and for investigating the 5mC or 6mA methylation-mediated mechanism underlying host response.

scholarly journals A comprehensive transcriptome data of normal and Nosema ceranae-stressed midguts of Apis mellifera ligustica workers

Data in Brief ◽  
2019 ◽  
Vol 26 ◽  
pp. 104349 ◽  
Author(s):  
Huazhi Chen ◽  
Yu Du ◽  
Cuiling Xiong ◽  
Yanzhen Zheng ◽  
Dafu Chen ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Nosema Ceranae ◽  
Transcriptome Data ◽  
Apis Mellifera Ligustica

scholarly journals Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers’ midguts

2020 ◽  
Author(s):  
Huazhi Chen ◽  
Xiaoxue Fan ◽  
Yu Du ◽  
Yuanchan Fan ◽  
Jie Wang ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Length Distribution ◽  
Quality Score ◽  
Nosema Ceranae ◽  
Full Length ◽  
Post Inoculation ◽  
Transcriptome Data ◽  
Fungal Parasite ◽  
Long Read ◽  
Colony Productivity

ABSTRACTApis mellifera ligustica is a subspecies of western honeybee, Apis mellifera. Nosema ceranae is known to cause bee microspodiosis, which seriously affects bee survival and colony productivity. In this article, Nanopore long-read sequencing was used to sequence N. ceranae-infected and un-infected midguts of A. m. ligustica workers at 7 d and 10 d post inoculation (dpi). In total, 5942745, 6664923, 7100161 and 6506665 raw reads were respectively yielded from AmT1, AmT2, AmCK1 and AmCK2, with average lengths of 1148, 1196, 1178 and 1201 bp, and N50 of 1328, 1394, 1347 and 1388 bp. The length distribution of raw reads from AmT1, AmT2, AmCK1 and AmCK2 was ranged from 1 kb to more than 10 kb. Additionally, the distribution of quality score of raw reads from AmT1 and AmT2 was among Q6∼Q12, while that from AmCK1 and AmCK2 was among Q6∼Q16. Further, 5745048, 6416987, 6928170, 6353066 clean reads were respectively gained from AmT1, AmT2, AmCK1 and AmCK2, and among them 4172542, 4638289, 5068270 and 4857960 were identified as being full-length. After removing redundant reads, the length distribution of remaining full-length transcripts was among 1 kb∼8 kb, with the most abundant length of 2 kb. The long-read transcriptome data reported here contributes to a deeper understanding of the molecular regulating N. ceranae-response of A. m. ligustica and host-fungal parasite interaction during microsporidiosis.

scholarly journals Immune Response of Eastern Honeybee Worker to Nosema ceranae Infection Revealed by Transcriptomic Investigation

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 728
Author(s):  
Wenhao Xing ◽  
Dingding Zhou ◽  
Qi Long ◽  
Minghui Sun ◽  
Rui Guo ◽  
...  
Keyword(s):  
Immune Response ◽  
Signaling Pathway ◽  
Apis Cerana ◽  
Enrichment Analysis ◽  
Nosema Ceranae ◽  
Pathway Enrichment Analysis ◽  
Post Inoculation ◽  
Sequencing Data ◽  
Humoral Immune ◽  
Immune Pathways

Here, a comparative transcriptome investigation was conducted based on high-quality deep sequencing data from the midguts of Apis cerana cerana workers at 7 d post-inoculation (dpi) and 10 dpi with Nosema ceranae and corresponding un-inoculated midguts. PCR identification and microscopic observation of paraffin sections confirmed the effective infection of A. c. cerana worker by N. ceranae. In total, 1127 and 957 N. ceranae-responsive genes were identified in the infected midguts at 7 dpi and 10 dpi, respectively. RT-qPCR results validated the reliability of our transcriptome data. GO categorization indicated the differentially expressed genes (DEGs) were respectively engaged in 34 and 33 functional terms associated with biological processes, cellular components, and molecular functions. Additionally, KEGG pathway enrichment analysis showed that DEGs at 7 dpi and 10 dpi could be enriched in 231 and 226 pathways, respectively. Moreover, DEGs in workers’ midguts at both 7 dpi and 10 dpi were involved in six cellular immune pathways such as autophagy and phagosome and three humoral immune pathways such as the Toll/Imd signaling pathway and Jak-STAT signaling pathway. In addition, one up-regulated gene (XM_017055397.1) was enriched in the NF-κB signaling pathway in the workers’ midgut at 10 dpi. Further investigation suggested the majority of these DEGs were engaged in only one immune pathway, while a small number of DEGs were simultaneously involved in two immune pathways. These results together demonstrated that the overall gene expression profile in host midgut was altered by N. ceranae infection and some of the host immune pathways were induced to activation during fungal infection, whereas some others were suppressed via host–pathogen interaction. Our findings offer a basis for clarification of the mechanism underlying the immune response of A. c. cerana workers to N. ceranae infection, but also provide novel insights into eastern honeybee-microsporodian interaction.

scholarly journals Comprehensive transcriptome data of normal and Ascosphaera apis-infected western honeybee larval guts

2020 ◽  
Author(s):  
Yu Du ◽  
Jie Wang ◽  
Zhiwei Zhu ◽  
Haibin Jiang ◽  
Xiaoxue Fan ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Gc Content ◽  
List Type ◽  
Sequencing Data ◽  
Illumina Hiseq ◽  
Ascosphaera Apis ◽  
Apis Mellifera Ligustica ◽  
Host Pathogen Interaction ◽  
Non Coding Rna ◽  
Host Pathogen

ABSTRAmTApis mellifera ligustica is a well-known subspecies of western honeybee, Apis mellifera. Ascosphaera apis is a common fungal pathogen of honeybee larvae, resulting in Chalkbrood disease. In this article, deep sequencing of un-treated 4-, 5-, and 6-day-old larval guts (AmCK1, AmCK2, AmCK3) and A. apis-treated 4-, 5- and 6-day-old larval guts (AmT1, AmT2, AmT3) of Apis mellifera ligustica were conducted using Illumina HiSeq™ 4000 platform. In total, 85811046, 81962296, 85636572, 79267686, 82889882, and 100211796 raw reads were respectively yielded from above-mentioned six groups. The result of sequencing satuation analysis suggested that the sequencing depth in this work was enough to detect nearly all expressed genes. After quality control, 85739414, 81896402, 85573798, 79202304, 82828926, and 100128692 clean reads were obtained. Additionally, the GC content of each group was above 45.26%. Furthermore, 47035852, 65612676, 71803878, 62560904, 65018360, and 56278272 clean reads were mapped to the Apis mellifera genome, including 41221479, 61172916, 66724233, 57531335, 60245732, and 52638986 unique mapped clean reads, and 2078427, 986825, 915375, 1082925, 1097130, and 716436 multiple mapped clean reads. In addition, exons were the most abundant regions mapped by clean reads, follow by intergenic regions and introns. The strand-specific cDNA library-based RNA sequencing data documented here will faciliate study on molecualr mechanisms underlying host immune response and host-pathogen interaction during chalkbrood disease, and benefit understanding of non-coding RNA-mediated cross-kingdom regulation between A. m. ligustica larvae and A. apis.Value of the DataThis data reported here could be used to explore circRNAs, lncRNAs, mRNAs and their competing endogenous RNA networks involved in response of western honeybee larvae to Ascosphaera apis infection.The current data contributes to better understanding mechanisms regulating host-pathogen interaction during chalkbrood disease.Our data can provide novel insights into understanding non-coding RNA-mediated cross-kingdom regulation between Apis mellifera ligustica and A. apis.

pH-Dependent Thermal Stability of Vibrio cholerae L-asparaginase

2019 ◽  
Vol 26 (10) ◽  
pp. 743-750 ◽  
Author(s):  
Remya Radha ◽  
Sathyanarayana N. Gummadi
Keyword(s):  
Vibrio Cholerae ◽  
Conformational Changes ◽  
Kinetic Studies ◽  
Structural Features ◽  
Structure Stability ◽  
Kcal Mole ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Ph Dependent ◽  
Ph Range

Background:pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.Objective:The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.Methods:Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.Results:The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.Conclusion:The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0–7.0.

Application of Nitrogen Heterocyclic Carbenes in Organocatalysis

2020 ◽  
Vol 09 ◽  
Author(s):  
Minita Ojha ◽  
R. K. Bansal
Keyword(s):  
Asymmetric Catalysis ◽  
Building Blocks ◽  
Structural Features ◽  
Heterocyclic Carbenes ◽  
Stetter Reaction ◽  
Metal Pollutants ◽  
Synthetic Strategy ◽  
Wide Range ◽  
Benzoin Condensation ◽  
Nitrogen Heterocyclic

Background: During the last two decades, horizon of research in the field of Nitrogen Heterocyclic Carbenes (NHC) has widened remarkably. NHCs have emerged as ubiquitous species having applications in a broad range of fields, including organocatalysis and organometallic chemistry. The NHC-induced non-asymmetric catalysis has turned out to be a really fruitful area of research in recent years. Methods: By manipulating structural features and selecting appropriate substituent groups, it has been possible to control the kinetic and thermodynamic stability of a wide range of NHCs, which can be tolerant to a variety of functional groups and can be used under mild conditions. NHCs are produced by different methods, such as deprotonation of Nalkylhetrocyclic salt, transmetallation, decarboxylation and electrochemical reduction. Results: The NHCs have been used successfully as catalysts for a wide range of reactions making a large number of building blocks and other useful compounds accessible. Some of these reactions are: benzoin condensation, Stetter reaction, Michael reaction, esterification, activation of esters, activation of isocyanides, polymerization, different cycloaddition reactions, isomerization, etc. The present review includes all these examples published during the last 10 years, i.e. from 2010 till date. Conclusion: The NHCs have emerged as versatile and powerful organocatalysts in synthetic organic chemistry. They provide the synthetic strategy which does not burden the environment with metal pollutants and thus fit in the Green Chemistry.

scholarly journals Ring-Forming Polymerization toward Perfluorocyclobutyl and Ortho-Diynylarene-Derived Materials: From Synthesis to Practical Applications

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1486
Author(s):  
Eugene B. Caldona ◽  
Ernesto I. Borrego ◽  
Ketki E. Shelar ◽  
Karl M. Mukeba ◽  
Dennis W. Smith
Keyword(s):  
Chemical Resistance ◽  
Structural Features ◽  
Review Article ◽  
Aryl Ether ◽  
Aromatic Rings ◽  
Practical Applications ◽  
Repeat Units ◽  
Wide Range ◽  
Synthetic Routes ◽  
The Cost

Many desirable characteristics of polymers arise from the method of polymerization and structural features of their repeat units, which typically are responsible for the polymer’s performance at the cost of processability. While linear alternatives are popular, polymers composed of cyclic repeat units across their backbones have generally been shown to exhibit higher optical transparency, lower water absorption, and higher glass transition temperatures. These specifically include polymers built with either substituted alicyclic structures or aromatic rings, or both. In this review article, we highlight two useful ring-forming polymer groups, perfluorocyclobutyl (PFCB) aryl ether polymers and ortho-diynylarene- (ODA) based thermosets, both demonstrating outstanding thermal stability, chemical resistance, mechanical integrity, and improved processability. Different synthetic routes (with emphasis on ring-forming polymerization) and properties for these polymers are discussed, followed by their relevant applications in a wide range of aspects.

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