DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species

BACKGROUND: Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. RESULTS: The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. CONCLUSIONS: This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.

High-throughput sequencing analysis of intestinal flora diversity of two freshwater snails (Radix auricularia and Planorbella trivolvis) / 生物工程学报

Freshwater snail is an important biological group in aquatic ecosystem and an intermediate host of many parasites. Intestinal flora plays an important role in animal energy metabolism and resistance to pathogens. We analyzed the intestinal microbiota diversity of Radix auricularia (RA) and Planorbella trivolvis (PL) by 16S rRNA high-throughput sequencing. At the phylum level, RA had 23 phyla, including Proteobacteria (33.63%), Cyanobacteria (15.33%), Chloroflexi (13.95%), and Actinomycetes (12.99%). PL had 13 phyla, including Proteobacteria (54.88%), Bacteroidetes (28.49%), and Actinomycetes (7.65%). At the genus level, there were 445 genera in RA, including Pleurocapsa, Thiodictyon, Leptotrichia, and Nocardioides. There were 238 genera in PL, including Cloacibacterium, OM60NOR5_clade, Pseudomonas, and Rhodobacter. Ninety-three genera were the common core flora of the two snail species (all the samples were present), and 27 genera had an abundance greater than 0.5%. The structure of intestinal microbiota was significantly different between the two groups (P=0.027). We performed the functional prediction of intestinal microbiota using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), and the results show that the KEGG functional composition of the intestinal flora of the two snails was similar, and the abundance of the amino acid metabolism, carbohydrate metabolism and membrane transport were large. In summary, the intestinal microbiota of the two snails was high in diversity and significantly different, but there were a large number of common core flora.

Screening of Auricularia auricula strains for strong production ability of melanin pigments

Abstract Melanin pigments have great application value and development potential in food industry to use as nature functional food colorants. In initial study, twenty-two Auricularia auricula strains were screened for stronger production ability of melanin pigments by solid culture. Three A. auricula strains (RF201, QD2 and QD6) with higher pigment production capacity were selected for further study through submerged culture supplementing 1 g/L l-tyrosine. The maximal pigment yields of A. auricula RF201, QD2 and QD6 were 493.9, 367.6 and 318.5 mg/L, respectively. Among three strains, A. auricula RF201 possessed the strongest production ability of melanin pigments. The present study indicated that A. auricula RF201 could be used as potential excellent producer of melanin pigments.

Influence of Temperature on the Bacterial Community in Substrate and Extracellular Enzyme Activity of Auricularia cornea

Temperature is an important environmental factor that can greatly influence the cultivation of Auricularia cornea. In this study, lignin peroxidase, laccase, manganese peroxidase, and cellulose in A. cornea fruiting bodies were tested under five different temperatures (20 °C, 25 °C, 30 °C, 35 °C, and 40 °C) in three different culture periods (10 days, 20 days and 30 days). In addition, the V4 region of bacterial 16S rRNA genes in the substrate of A. cornea cultivated for 30 days at different temperatures were sequenced using next-generation sequencing technology to explore the structure and diversity of bacterial communities in the substrate. Temperature and culture days had a significant effect on the activities of the four enzymes, and changes in activity were not synchronized with changes in temperature and culture days. Overall, we obtained 487,694 sequences from 15 samples and assigned them to 16 bacterial phyla. Bacterial community composition and structure in the substrate changed when the temperature was above 35 °C. The relative abundances of some bacteria were significantly affected by temperature. A total of 35 genera at five temperatures in the substrate were correlated, and 41 functional pathways were predicted in the study. Bacterial genes associated with the membrane transport pathway had the highest average abundance (16.16%), and this increased at 35 °C and 40 °C. Generally, different temperatures had impacts on the physiological activity of A. cornea and the bacterial community in the substrate; therefore, the data presented herein should facilitate cultivation of A. cornea.

Development of a Molecular Marker for Fruiting Body Pattern in Auricularia auricula-judae

The fruiting body pattern is an important agronomic trait of the edible fungus Auricularia auricula-judae, and an important breeding target. There are two types of fruiting body pattern: the cluster type and the chrysanthemum type. We identified the fruiting body pattern of 26 test strains, and then constructed two different near-isogenic pools. Then, we developed sequence characterized amplified region (SCAR) molecular markers associated with the fruiting body pattern based on sequence-related amplified polymorphism (SRAP) markers. Ten different bands (189–522 bp) were amplified using 153 pairs of SRAP primers. The SCAR marker “SCL-18” consisted of a single 522-bp band amplified from the cluster-type strains, but not the chrysanthemum strains. This SCAR marker was closely associated with the cluster-type fruiting body trait of A. auricula-judae. These results lay the foundation for further research to locate and clone genes controlling the fruiting body pattern of A. auricula-judae.

Extraction, isolation, and identification of a new lectin from Tibetan medicine Auricularia auricula / 中草药

Objective To extract and isolate the lectin from Tibetan medicine Auricularia auricula. Methods The lectin from Tibet A. auricula was separated by sephadex column chromatography and ion exchange chromatography, and then its relative molecular weight was determinated by using matrix assisted laser desorption ionization time of flight mass spectrometry (5 800 MALDI-TOF/TOF). N-terminal sequential detection results suggested the amino acid sequences by comparing with the UniProt database. Results A kind of lectin was obtained from the separation of Tibet A. auricula with the molecular weight of of 18 913.22, in which the N- terminal amino acid sequence was detected as ITAPTTTSSAATE by the full automatic protein polypeptide sequencing instrument. The amino acid sequences of four peptide fragments were QIDAERK, TNHSVVTWNDK, RLNFTAGNPFPR, and VRELEQQVDSMTK. Conclusion These sequences are not found in the existing protein database of A. auricula, indicating that the isolated lectin should be a new type protein and it is confirmed as a new kind of lectin.

Effect of microbial fermentation on total sugar content and in vitro hypolipidemic effect of Auricularia auricula / 中草药

Objective To study the effect of microbial action on total sugar content and the in vitro hypolipidemic effect of Auricularia auricula, and to screen out the bacteria which can enhance the lipid-lowering function. Methods Through the fermentation of A. auricula, the total sugar content of the fermenting liquid of A. auricula was detected, and the total cholesterol extraction, the amount of cholesterol adsorption in vitro, the adsorption amount of sodium cholate in vitro, and the binding of sodium cholate in vitro were used as indexes to analyze the change of lipid-lowering capacity. Results Data analysis showed that Bifidobacterium and Saccharomyces cerevisiae compound had the greatest effect on the lipid-lowering function of A. auricula, and the total sugar content was increased by 146.58% compared with the pre-fermentation water extract. The extracorporeal cholesterol absorption, in vitro sodium cholate absorption, and sodium cholate binding were increased by 110.04%, 4.44%, and 27.66% respectively in comparison with the pre-fermentation water extract, and increased by 122.58%, 4.07%, and 60.02%, respectively when compared with the pre-fermentation ethanol extract. Conclusion The mixed fermentation of Bifidobacterium and Saccharomyces cerevisiae can significantly improve the total sugar content and hypolipidemic effect of A. auricula.

Optimization of culture medium for production of melanin by Auricularia auricula

Abstract Melanin is a natural high molecular weight pigment with the huge application value and development potential in food industry. In the present study, medium composition for melanin production by fungus Auricularia auricula was investigated. Wheat bran extract, l-tyrosine, and CuSO4 were determined to optimize medium composition by response surface methodology with Box-Behnken design. Results indicated that the optimal medium composition was 26.80% (v/v) wheat bran extract, 1.59 g/L l-tyrosine, and 0.11 g/L CuSO4, and the maximum melanin yield was 519.54 mg/L. Melanin production through A. auricula fermentation avoided expensive enzymatic or complicated chemical methods for melanin extraction from tissues of plant or animal, which had the huge application value and development potential for efficient production of melanin.

Protective effect of Auricularia auricular-judae polysaccharide on pulmo-nary tissues of rats with LPS-induced acute lung injury / 中国病理生理杂志

AIM:To investigate the effects of Auricularia auricular-judae polysaccharide ( AAP) on pulmonary tissues of rats with LPS-induced acute lung injury (ALI) and its mechanisms.METHODS: Adult Sprague-Dawley rats were randomly divided into control group , LPS group, low-dose AAP group, middle-dose AAP group, high-dose APP group, and dexamethasone group.The rats were injected with LPS (8 mg/kg, ip) to induce ALI.The rats in the AAP groups were treated with AAP for 7 d before the induction of ALI .The protein concentration in the bronchoalveolar lavage fluid (BALF) was measured.The lung edema degree was measured by detecting the wet /dry weight ratio.The myeloper-oxidase ( MPO) , total antioxidant capacity ( T-AOC) , total superoxide dismutase ( T-SOD) , nitric oxide synthase ( NOS) and malondialdehyde ( MDA) levels were determined .The pathological changes of the lung tissues were evaluated by HE staining.RESULTS:Treatment with AAP significantly improved LPS-induced lung pathological changes , attenuated the protein concentration in the BALF and wet/dry weight ratio , inhibited the activities of MPO and NOS , reduced MDA level and increased the activities of T-AOC and T-SOD.CONCLUSION: AAP protects against LPS-induced acute lung injury in rats.

Studies on Ear Fungus-Auricularia from the Woodland of Nameri National Park, Sonitpur District, Assam.

Auricularia is the genus of the order Auriculariales with more than 10 species. It is also called ear fungus due to its morphological similarities with human ear and has considerable mythological importance. Auricularia auricula is the type species of the order Auriculariales. Different species of Auricularia are edible and some have medicinal importance and still investigations are going on other species to find out their medicinal properties. Extensive woodland of Nameri National Park provides ideal condition for the growth of different species of Auricularia. In this context the present study has been undertaken to study the taxonomy and diversity of different species of Auricularia and bring together information of its ethenomycological uses. As a result of field and laboratory study four different species of Auricularia were collected of which 3 species were identified and one species remain unidentified.

Morphological and Molecular Characterization of Lymnaeid Snails and Their Potential Role in Transmission of Fasciola spp. in Vietnam

Freshwater snails of the family Lymnaeidae play an important role in the transmission of fascioliasis worldwide. In Vietnam, 2 common lymnaeid species, Lymnaea swinhoei and Lymnaea viridis, can be recognized on the basis of morphology, and a third species, Lymnaea sp., is known to exist. Recent studies have raised controversy about their role in transmission of Fasciola spp. because of confusion in identification of the snail hosts. The aim of this study is, therefore, to clarify the identities of lymnaeid snails in Vietnam by a combination of morphological and molecular approaches. The molecular analyses using the second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA clearly showed that lymnaeids in Vietnam include 3 species, Austropeplea viridis (morphologically identified as L. viridis), Radix auricularia (morphologically identified as L. swinhoei) and Radix rubiginosa (morphologically identified as Lymnaea sp.). R. rubiginosa is a new record for Vietnam. Among them, only A. viridis was found to be infected with Fasciola spp. These results provide a new insight into lymnaeid snails in Vietnam. Identification of lymnaeid snails in Vietnam and their role in the liver fluke transmission should be further investigated.

Research on change of S180 tumor cell membrane function by Auricularia polytricha polysaccharides / 中国药学杂志

OBJECTIVE: Auricularia polytricha is paid great attention to as an anticancer food, of which polysaccharide is an important functional component. The anticancer mechanism of Auricularia polytricha polysaccharide is critically important to its development and usage. METHODS: Five polysaccharides were isolated using counter-current chromatography and DEAE column chromatography from the wild Auricularia polytricha. RESULTS: AAPS1, AAPS2 and AAPS3 were light yellow floc, and AAFRB and AAFRC were white powder. The activities of the 5 polysaccharides on S180 sarcoma cell membrane were analyzed, and they could significantly change the characteristic of the tumor cell membrane, resulting in more free fatty acids. Among the 5 polysaccharides, AAPS2 showed the highest activity. The polysaccharides significantly lowered the levels of sialic acid (SA) in the cell membrane of tumor-bearing mice (P < 0.01), and AAPS2 had the highest activity than those of others. The polysaccharide AAPS2 could significantly alter membrane fluidity (P < 0.05). CONCLUSION: The anti-tumor mechanism may be related to the membrane glycoprotein and glycolipids chain terminal residues SA, and the peroxidation of lipid in cell membrane. Copyright 2012 by the Chinese Pharmaceutical Association.

Slippery Scar: A New Mushroom Disease in Auricularia polytricha

A new disease, the slippery scar, was investigated in cultivated bags of Auricularia polytricha. This fungus was isolated from the infected mycelia of cultivated bags. Based on morphological observation, rDNA-internal transcribed spacer and 18S sequence analysis, this pathogen was identified as the Ascomycete Scytalidium lignicola. According to Koch's Postulation, the pathogenicity of S. lignicola to the mycelia of A. polytricha was confirmed. The parasitism of this fungus on mushroom mycelia in China has not been reported before.

Protective effects of auricularia auricular polysaccharide on chronic cerebral ischemia injury in rats / 中国病理生理杂志

AIM: To investigate the effects of auricularia auricular polysaccharide (AAP) on chronic cerebral ischemia injury in rats. METHODS: The chronic cerebral ischemia mode1 was made by permanent middle cerebral artery occlusion (MCAO) on the right side. AAP at different doses (50 mg/kg and 100 mg/kg) was intragastrically administered at the onset of ischemia and in the following days after operation, once a day for 4 weeks. After 4 weeks of MCAO, Morris water maze test was introduced to examine the learning and memory functions. Nissl staining was performed to detect the survival neurons in hippocampal slices. Level of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) in brain tissue were measured. RESULTS: Rats treated with AAP showed a shorter escaping latency in spacial navigation test because the AAP treated rats spent less time to find the platform in spatial probe test. More survival neurons in hippocampal slices were observed from AAP treated rats. Also, the MDA level in brain tissue was reduced and SOD activity in brain tissue was increased in the AAP treated rats with MCAO. CONCLUSION: AAP protects rats from chronic brain ischemic injury, in which its anti-oxidative effect might be involved.

Development of Detection Methods for Cellulolytic Activity of Auricularia auricula-judae

To obtain basic information on the detection of cellulolytic activity in Auricularia auricula-judae, the influences of dye reagent, pH, and temperature were assessed. Chromogenic dye (congo red, phenol red, remazol brilliant blue, and trypan blue) was individually incorporated into a medium containing either carboxymethyl-cellulose, Avicel, or D-cellobiose as a polysaccharide carbon substrate. The other assessments utilized pHs ranging from 4.5 to 8.0 and temperatures from 15~35degrees C. Overall, when A. auricula-judae species were transferred onto media contained Congo red and adjusted pH 7.0 and then incubated at 25degrees C for 5 days, the clear zone indicative of cellulolytic activity was more pronounced.

Study on the antithrombotic effect of polysaccharide of Auricularia auriculajudae / 中国生化药物杂志

Purpose To study on the antithrombotic effect of polysaccharide of Auricularia auriculajudae.Methods The method of hot water extraction for extracting polysaccharide from Auricularia auriculajudae was used. The antithrombotic effect was studied by animal experiments.The length and the weight of arterial thrombosis were determined. Characteristic thrombus formation time (CTFT), and thrombus formation time (TFT),the rate of platelet adhesion and the blood viscosity were determined also.Results As compared with the normal saline group,polysaccharide of Auricularia auriculajudae(ig) remarkedly prolonged CTFT and TFT.The length of thrombus was shortened. Thrombus wet weight, thrombus dry weight,and blood viscosity were decreased, yet had no significant influence on the rate of platelet adhesion.Conclusion Polysaccharides of Auricularia auriculajudae can significantly inhitit the formation of thrombus.

Effect of Auricularia auricular polysaccharide on ischemia myocardial injury / 中国病理生理杂志

AIM: To investigate the protective effect of auricularia auricular polysaccharide (AAP) on the myocardial injury induced by ischemia and its underlying mechanism. METHODS:AAP was orally administrated to rats at the does of 50, 100 or 200 mg·kg~(-1)·d~(-1) for 20 d. Myocardial injury was induced in anesthetized Sprague - Dawley rats by left anterior descending coronary artery ligation. Myocardial infarct size, the level of lactate dehydrogenase (LDH), the activity of superoxide dismutase (SOD) , the production of lipid peroxidation malondialdehyde (MDA) and protein level of myocardial collagen of the heart were measured. RESULTS: The average myocardial infarct size in AAP groups was significantly smaller than that in ischemia group. The level of serum LDH induced by regional myocardial ischemia was significantly decreased in AAP group compared to ischemia group ( P < 0.01). AAP inhibited the production of MDA and increased the activity of SOD. Furthermore, AAP reduced the protein level of myocardial collagen after ischemia (P < 0.01).CONCLUSION: AAP prevents myocardium from ischemia injury as an antioxidant.

Nursing study on treating Ⅱ toⅢphase pressure sore of senior citizen by compatibility of auricularia in-depth fermentation extracts and the dimethyl acrylyl hydropathic compress / 中国实用护理杂志

Objective To study the effect of the compatibility on treating Ⅱ toⅢphase pressure sore of senior citizen by auricularia in-depth fermentation extracts and the dimethyl acrylyl hydropathic compress.Methods A total of 60 patients with Ⅱto Ⅲ phase pressure sore were divided randomly into the expedmental group and the control group with 30 cases in each group.The experimental group(30 cases.50 pressure sores)were treated with the auricularia in--depth fermentation extracts and the dimethyl acrylyl hydropathic compress.The control group(30 case8,46 pressure sores)were treated with conventional methods of dressing change,0.5% iodine to disinfect the wound surface.then bounded it up with the aseptic vaseline yarn and the sursical dressing.The curative effect Was compared by observing the effect indicators.Results The response rate of the experimental group was 100.0%.with an average healing time of 10.33 d.For the control group.the response rate was 78.3%,the average healing time Was 24.27 d.There Was significant difference on efficiency and the average healing time between the two groups,P<0.01.Conclusions Auricularia in-depth fermentation extracts and the dimethyl acrylyl hydropathic compress to treat the senior citizen Ⅱ toⅢphase pressure gore with a view to easy.safe and economical characteris tic.has a significant effect on the new agricultural co-medical health care and community groups.

Hypolipidemic Effects of Biopolymers Extracted from Culture Broth, Mycelia, and Fruiting Bodies of Auricularia auricula-judae in Dietary-induced Hyperlipidemic Rats

Hypolipidemic effect of biopolymers extracted from culture broth (CP), mycelia (MP), and fruiting bodies (FP) of Auricularia auricula-judae was investigated in dietary-induced hyperlipidemic rats. The experimental animals were administrated (100 mg/kg body weight) with different biopolymers, daily for 4 weeks. Hypolipidemic effects were achieved in all the experimental groups, however, FP was proved to be the most potent one. The administration of the FP reduced the plasma triglyceride, total cholesterol, low-density lipoprotein cholesterol, and atherogenic index by 24.3, 28.5, 36.4, and 40.9%, respectively, while increased the high-density lipoprotein cholesterol level (9.0%), when compared to the saline (control) administered group.

STUDY ON PHYSICOCHEMICAL PROPERTY OF THE COMPONENT-FE COMPLEX OF AURICULARIA AURICULA / 营养学报

Objective To compare the chemical composition of Auricularia auricula polysaccharide and the colloid, and the property of the different component-Fe complex. Method Auricularia auricula polysaccharide and the colloid were prepared first, then Auricularia auricula polysaccharide iron complex (APIC)and Aurcularia auricula glia iron complex (AGIC) were synthesized respectively with FeCl3 under alkaline condition, and their physicochemical property was determined. Results The stablility of AGIC was better than APIC and AGIC could be reduced to Fe(Ⅱ)by ascorbic acid more easily. Conclusion The Auricularia auricula colloid could combine with Fe(Ⅲ)easier than the polysaccharide, and would be expected to become a higher bioavailable iron-supplement.