ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding

Influence of nitrogen substitution at an equivalent total nitrogen level on bacterial and fungal communities, as well as enzyme activities of the ditch bottom soil in a rice-fish coculture system

BACKGROUND

Rice-fish coculture system (RFS) operates through effectively utilizing water and land resources in a complementary form, but it requires more efficient utilization of fertilizer and feed without compromising rice yield. However, the knowledge of how to regulate the proportion of nitrogen (N) supplied from fertilizer and feed at an equivalent total N level to improve the benefits of RFS remains limited. Therefore, four treatments (S0: RFS with 0% N from fertilizer and 100% N from feed; S25: RFS with 25% N from fertilizer and 75% N from feed; S50: RFS with 50% N from fertilizer and 50% N from feed; S75: RFS with 75% N from fertilizer and 25% N from feed) were conducted to assess the variation of ditch bottom soil properties, microbial communities and enzyme activities, as well as to obtain the optimal ratio of N supplied from fish feed and fertilizer.

RESULTS

The experiments showed that the contents of soil organic matter, total carbon and total N, and the activities of urease, N-acetyl-β-D-glucosaminidase, protease, β-1,4-glucosidase and catalase in the ditch bottom soil significantly reduced in S25 treatment, compared with the other three treatments. Ammonium N content decreased with increasing percentage of the basal fertilizer, whereas nitrate N content and pH value showed an adverse trend. However, the bacterial and fungal communities were unaffected by the ratio shifts between fertilizer-N and feed-N, but their dominant phyla were influenced by the ditch bottom soil N level. Moreover, the bacterial community composition was positively related to nitrate N, whereas fungal diversity was positively correlated with pH, ammonium N and nitrate N, and urease. We also found that the treatment of N input with 25% N from fertilizer and 75% N from feed can reduce N deposition in the ditch bottom soil in the rice-fish coculture system.

CONCLUSION

Our findings indicate that under the equivalent total N input level, the relative higher ratio of N from fish feed increased (S0 treatment) or reduced (S25 treatment) the deposition of N in the ditch bottom soil, and improved fish production, but decreased rice yield; while the higher ratio of N from basal fertilizer increased the transportation of nutrients into the ditch bottom soil and rice yield, but reduced fish production. So when considering multi-balance and multiple benefits, we recommend that a selective substitution ratio within 50% ~ 75% from fish feed to substitute for the basal fertilizer under the equivalent total N input may achieve a good balance of rice and fish production improvement, and reduce nutrients wastage to the ditch bottom, as well as alleviate the potential of non-point source pollution. This study also provides an evidence for regulating and optimizing the ratio of N supplied from fertilizer and fish feed at an equivalent total N level through monitoring the nutrient accumulation in ditch bottom soil in the rice-fish coculture system. © 2024 Society of Chemical Industry.

Moss-dominated biocrust-based biodiversity enhances carbon sequestration via water interception and plant-soil-microbe interactions

We investigated a nature-based solution (NbS) via incorporating biocrust into alfalfa-maize intercropping system to test carbon sequestration in seriously eroded agricultural soils. Field investigation showed that the NbS (moss-dominated biocrust + intercropping) massively lowered surface soil erosion by 94.5% and soil carbon (C) and nitrogen (N) loss by 94.7 and 96.8% respectively, while promoting rainwater interception by 82.2% relative to bare land (CK). There generally existed positive interactions between biocrust and cropping in the integrated standing biodiversity system. Enhanced plant biomass input into soils substantially promoted soil fungal community diversity and abundance under NbS (p < 0.05). This enabled NbS to evidently improve soil macroaggregate proportion and mean weight diameter. Critically, topsoil carbon storage was increased by 2.5 and 10.7%, compared with CK and pure intercropping (p < 0.05). Conclusively, the standing diversity under such NbS fostered soil C sequestration via water interception and plant-soil-microbe interactions in degraded agricultural soils.

Molecular Characterization of Wild and Cultivated Strawberry (Fragaria × ananassa) through DNA Barcode Markers

Background

DNA barcoding is a useful technique for the identification, conservation, and diversity estimation at the species level in plants. The current research work was carried out to characterize selected Fragaria species from northern Pakistan using DNA barcode markers. Methodology. Initially, the efficacy of eight DNA barcode markers was analyzed based on the amplification and sequencing of the genome of selected Fragaria species. The resultant sequences were analyzed using BLAST, MEGA 7.0, and Bio Edit software. The phylogenetic tree was constructed by using Fragaria current species sequences and reference sequences through the neighbor-joining method or maximum likelihood method.

Results

Among eight DNA barcode markers, only two (ITS2 and rbclC) were amplified, and sequences were obtained. ITS2 sequence was BLAST in NCBI for related reference species which ranged from 89.79% to 90.05% along with Fragaria vesca (AF163517.1) which have 99.05% identity. Similarly, the rbclC sequence of Fragaria species was ranged from 96% to 99.58% along with Fragaria × ananassa (KY358226.1) which had 99.58% identity.

Conclusion

It is recommended that DNA barcode markers are a useful tool to identify the genetic diversity of a species. Moreover, this study could be helpful for the identification of the Fragaria species cultivated in other regions of the world.

DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances

Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.

Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.

The Garbage Enzyme with Chinese Hoenylocust Fruits Showed Better Properties and Application than When Using the Garbage Enzyme Alone

Garbage enzyme (GE) is a vinegar or alcohol product derived from fermenting fresh kitchen waste, such as vegetable and fruit residues (peels, cuttings and bits), sugar (brown sugar, jaggery or molasses sugar) and water. Chinese honeylocust fruits (Gleditsia sinensis) have been used in China for at least 2000 years as a detergent. The aim of the study was to investigate the properties and application of Chinese honeylocust garbage enzyme (CHGE), which is produced when equal amounts of Chinese honeylocust fruits and fresh wastes are mixed. The results showed that CHGE had lesser microbial communities and lower surface tension than GE. CHGE also had higher viscosity, foam stability and emulsion stability than GE. Compared with GE, CHGE induced higher enzymatic amylase, cellulase, lipase and protease activities. CHGE had stronger detergency than GE and a 100× dilution of CHGE could significantly remove pesticide residues after a 30 min soaking treatment. The study showed that as a biological detergent, CHGE is safer and more environmentally friendly than GE and has remarkable washing and cleaning power. The preparation method of the detergent is simple: it can be prepared at home using fruit and vegetable waste, which is beneficial to the secondary utilization of waste and the reduction of pollution to the environment and damage to human health.

Specification and DNA Barcoding of Thai Traditional Remedy for Chronic Kidney Disease: Pikad Tri-phol-sa-mut-than

The Pikad Tri-phol-sa-mut-than (TS) remedy, a Thai traditional medicine, is officially recorded in Tamra Paetsart Sonkrau Chabub Anurak for its capabilities in treating kidney deficiency. TS remedy is composed of three fruit species—Aegle marmelos (L.) Corrêa., Coriandrum sativum L., and Morinda citrifolia L.—in an equal part by weight. The quality of the raw material is one of the essential factors that can affect the effectiveness and safety of treatment by herbal remedy. The pharmacognostic evaluation and DNA barcode of the three fruit species and TS remedy were performed in this study to authenticate them from contamination, and to provide the scientific database for further uses. Macroscopic and microscopic examination, chemical profile by TLC, and DNA barcoding were employed to positively identify the raw materials bought from the herbal market, especially the powder form. Consequently, the outcomes of this investigation can be used to develop an essential and effective tool for the authentication of crude drugs and herbal remedies.

The preliminary evaluation of differential characteristics and factor evaluation of the microbial structure of rural household toilet excrement in China

Recent studies on the microbial community composition of human excrement after rural household toilet treatment are unclear regarding the effects and risks of using recycled products as fertilizers in agriculture. In this study, we used Illumina high-throughput sequencing to investigate the microbial community structure of the excrement from 50 Chinese rural household toilets on a spatial scale, and we evaluated the impact of select geochemical factors on the bacterial and fungal communities in the human excrement. Multivariate analysis showed that there was a significant spatial differentiation of the human excrement in microbial communities after all toilet treatments. Twenty dry toilet samples and thirty septic tank samples had similar bacterial (Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes) and fungal phyla (Ascomycota and Basidiomycota), differing only in the proportions of the microorganisms. For both dry toilet samples and septic tank samples, the pH and ammonium nitrogen were found to be the major driving forces affecting the changes in bacterial community structures (p<0.05), while there was no correlation found for the fungal community with environmental factors in China (p>0.05), except in the northern regions, where the total phosphorus was found to be significantly correlated with the fungal community (p<0.05). Network analysis confirmed that NH4+-N had the most significant impact on the content of pathogens. Certain pathogens were still detected after toilet treatment, such as Streptococcus, Bacteroides, Aspergillus, and Chrysosporium, and the proportion of potential pathogenic bacteria in dry toilets was higher than that in septic tanks, suggesting that septic tanks were better than dry toilets in treating human excrement. These results provide an ecological perspective for understanding the large-scale geographic distribution of household excrement microbial communities in rural areas and for improving human excrement treatment technologies and avoiding the risks of agricultural applications.

New Insights Into the Skin Microbial Communities and Skin Aging

Although it is well-known that human skin aging is accompanied by an alteration in the skin microbiota, we know little about how the composition of these changes during the course of aging and the effects of age-related skin microbes on aging. Using 16S ribosomal DNA and internal transcribed spacer ribosomal DNA sequencing to profile the microbiomes of 160 skin samples from two anatomical sites, the cheek and the abdomen, on 80 individuals of varying ages, we developed age-related microbiota profiles for both intrinsic skin aging and photoaging to provide an improved understanding of the age-dependent variation in skin microbial composition. According to the landscape, the microbial composition in the Children group was significantly different from that in the other age groups. Further correlation analysis with clinical parameters and functional prediction in each group revealed that high enrichment of nine microbial communities (i.e., Cyanobacteria, Staphylococcus, Cutibacterium, Lactobacillus, Corynebacterium, Streptococcus, Neisseria, Candida, and Malassezia) and 18 pathways (such as biosynthesis of antibiotics) potentially affected skin aging, implying that skin microbiomes may perform key functions in skin aging by regulating the immune response, resistance to ultraviolet light, and biosynthesis and metabolism of age-related substances. Our work re-establishes that skin microbiomes play an important regulatory role in the aging process and opens a new approach for targeted microbial therapy for skin aging.

Applied Barcoding: The Practicalities of DNA Testing for Herbals

DNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation of DNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change in status, requiring the establishment of standardized, reliable and reproducible methods. The process by which this can be achieved for any herbal medicine is described, using Hypericum perforatum L. (St John's Wort) and potential adulterant Hypericum species as a case study. A range of practical issues are considered including quality control of DNA sequences from public repositories and the construction of individual curated databases, choice of DNA barcode region(s) and the identification of informative polymorphic nucleotide sequences. A decision tree informs the structure of the manuscript and provides a template to guide the development of future DNA barcode tests for herbals.

Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint

The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.

Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models

Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.

Seasonal variations of microbial assemblage in fine particulate matter from a nursery pig house

The microorganisms contained in PM_2.5 from livestock houses can spread over long distances through airborne transmission. As such, the potential bacterial pathogens and fungal allergens within can pose a formidable threat to nearby residents' health and the overall environment. However, little is known about the microbial assemblage contained in PM_2.5 from pig houses. In this study, 16S and 18S rRNA gene sequencing was employed to analyze the bacterial and fungal assemblage contained in PM_2.5 from a nursery pig house across four seasons, respectively. The results showed that alpha diversity was higher in summer and autumn compared to the spring and winter. The bacterial and fungal assemblage varied according to season. At the phylum level, the dominant bacteria and fungi were Firmicutes and Basidiomycota, respectively, across the four seasons. At the genus level, a total of five potential bacterial pathogen and 20 potential fungal allergen genera were identified across the samples. The most abundant bacterial pathogen and fungal allergen genera were observed in summer and autumn, respectively, but neither had a significant correlation with PM_2.5 concentration. Moreover, microbial diversity and the relative abundance of fungal allergen genera were positively correlated with temperature and relative humidity. It can be concluded that microbial diversity and assemblage varied significantly among the seasons in a nursery pig house, and this can be useful in exploring the potential risks of PM_2.5 from pig houses across all four seasons.

Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)

BACKGROUND AND AIMS

Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.

METHODS

We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing.

KEY RESULTS

Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models.

CONCLUSIONS

Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.

Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study

Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.

Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure

Ligustici Rhizoma et Radix (LReR), an important Chinese medicine known as "Gao-ben," refers to Ligusticum sinense Oliv. or Ligusticum jeholense Nakai et Kitag. However, a number of other species are commonly sold as "Gao-ben" in the herbal medicine market, which may result in a series of quality control problems and inconsistent therapeutic effects. The "Gao-ben" is commonly sold sliced and dried, making traditional identification methods difficult. Here, the mini barcode ITS2 region was examined on 68 samples representing LReR and 7 potential adulterant or substitute species. The results showed 100% success rates of PCR and sequencing and the existence of a barcoding gap. The neighbor-joining (NJ) tree indicated that all the tested samples could be exactly identified. The ITS2 secondary structure revealed a clear difference between true "Gao-ben" and three adulterant species. We therefore recommend the use of ITS2 as a mini barcode for distinguishing between closely or distantly related plant species that may be used in Chinese medicine.

Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine

Southern Chinese Medicine (SCM) is an important sect of Traditional Chinese Medicine (TCM) with its own special cultural style. Species identification is essential for TCM quality control because authentic herbs are possibly substituted with adulterants that would threaten the health of the public or even cause death. Here, we provided the first local reference DNA barcode library based on the second internal transcribed spacer (ITS2) for the molecular identification of SCM. A total of 1512 specimens of southern herbs representing 359 species were collected under the instructions and identification of taxonomic experts. Genomic DNA was extracted, and the PCR reaction proceeded according to standard procedures. After Sanger sequencing, sequence assembling and annotation, a reliable ITS2 barcode library with 1276 sequences from 309 species of Southern herbs was constructed. The PCR efficiency of the whole samples was 84.39%. Characteristics of the ITS2 barcode were analyzed, including sequence lengths and GC contents in different taxa. Neighbor-joining trees based on Kimura 2-Parameter (K2P) genetic distances showed a 67.56% successful rate of species identification with ITS2 barcode. In addition, 96.57% of species could be successfully identified at the genus level by the BLAST method. Eleven plant species were discovered to be cryptic. In addition, we found that there is an incorrect sequence existing in the public database, making a reliable local DNA barcode reference more meaningful. ITS2 barcodes exhibit advantages in TCM identification. This DNA barcode reference library could be used in Southern Chinese Medicine quality control, thus contributing to protecting public health.

DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis

Background

The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left(\overline{\varDelta G}\right) $$\end{document}ΔG¯ were determined by an in silico analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G.

Results

The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the cry11Aa, Ba and Bb genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<∆G). In the region of domain III; this tendency was lower (>∆G) in the cry11Ba and Bb genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA.

Conclusion

These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the in silico design of cry gene assembly by DNA shuffling techniques.

Differential diagnosis and molecular characterization of Hymenolepis nana and Hymenolepis diminuta (Cestoda: Cyclophyllidea: Hymenolepididae) based on nuclear rDNA ITS2 gene marker

Given the widespread distribution and medical implication of members of the genus Hymenolepis, specific identification of the aetiological agent becomes imperative. For precise diagnosis of the species, molecular techniques such as PCR and RFLP of the nuclear ribosomal internal transcribed spacer 2 (rDNA-ITS2) gene marker were carried out. The results showed distinct restriction patterns for both Hymenolepis nana and Hymenolepis diminuta when digested with either of the enzymes RsaI, HaeIII or HhaI. The annotated rDNA-ITS2 sequences from the two species revealed differences in the length; the folded secondary structure also depicted clear demarcation between the two species with variations in length of the helices, pyrimidine-pyrimidine mismatches and sites where motifs occur. In phylogenetic analysis of the evolutionary relationship between the two species as well as with other members of the family Hymenolepididae, the species causing human hymenolepiasis were found to be distantly related as they diverged independently from the ancestral lineage.

DNA Barcoding Identification of Kadsurae Caulis and Spatholobi Caulis Based on Internal Transcribed Spacer 2 Region and Secondary Structure Prediction

Background:

Kadsurae Caulis and Spatholobi Caulis have very similar Chinese names. Their commodities were hard to distinguish because their stems were very alike after dried and processed. These two herbal drugs were often mixed in clinical use.

Objective:

Authenticity assurance is crucial for quality control of herbal drugs. Therefore, it is essential to establish a method for identifying the two herbs.

Materials and Methods:

In this paper, we used the DNA barcoding technology, based on the internal transcribed spacer 2 (ITS2) regions, to differentiate Kadsurae Caulis and Spatholobi Caulis.

Results:

The ITS2 of these two herbs were very different. They were successfully differentiated using the DNA barcoding technique.

Conclusions:

DNA barcoding was a promising and reliable tool for the identification of medicinal plants. It can be a powerful complementary method for traditional authentication.

SUMMARY

The internal transcribed spacer 2 (ITS2) regions between Kadsurae Caulis and Spatholobi Caulis varied considerably, totally 139 variable sites

Sample 1 was not Kadsurae Caulis as it labeled, but it should be Spatholobi Caulis in fact based on ITS2 region

The secondary structure can also separate Kadsurae Caulis and Spatholobi Caulis effectively

DNA barcoding provided an accurate and strong prove to identify these two herbs.

Abbreviations used: CTAB: hexadecyltrimethylammonium bromide, DNA: deoxyribonucleic acid, ITS2:internal transcribed spacer 2, PCR: polymerase chain reaction

Technical note: use of internal transcribed spacer for ruminal yeast identification in dairy cows

Molecular techniques are important tools for microbiological studies in different habitats, and the internal transcribed spacer (ITS) has been proved to be useful for analyzing fungal diversity. The aim of this study was to use the ITS region to generate ruminal yeast profile and to identify ruminal yeast. DNA from ruminal digesta was extracted to amplify the ribosomal ITS region. The profile from the PCR products was visualized and the excised bands from the profile were identified as the genera Millerozyma, Pichia, Rhizomucor and Hyphopichia. Overall, the ITS resulted to be a simple, fast and sensitive approach that allowed profiling and identification of ruminal yeast that have not been previously described (Millerozyma and Hyphopichia) in the rumen microbial community.