Traditional Morphological Methods Research Articles

Human and non-human bone identification using FTIR spectroscopy.

Human and non-human identification of unknown skeletal remains is of great importance in forensic and anthropologic contexts. However, the traditional morphological methods for bone species identification are subjective or time-consuming. Here, we utilized Fourier transform infrared (FTIR) spectroscopy and chemometric methods to determinate the spectral variances between human and non-human (i.e., pig, goat, and cow) bones. To simulate real forensic situations as much as possible, fresh, boiled, and decomposed bones were included in this study. Principal component analysis (PCA) results illustrated pig bones were more sensitive to the environmental and external factors than other species studied in this work. Thus, pig bone might not be a suitable proxy for human bone in the study of postmortem changes. More importantly, score plots of PCA results showed clear separation with a slight overlap between the human and non-human fresh bones, but it failed to distinguish the boiled and decomposed bones. Then, partial least squares discriminant analysis (PLS-DA) was employed, and both internal and external validations were conducted to assess its classification ability, which resulted in 99.72 and 99.53% accuracy, respectively. According to the loading plots of PCA and PLS-DA, the spectral diversity was mainly due to the inorganic portion (i.e., carbonates and phosphates), which can remain relatively stable under various conditions. As such, our results illustrate that FTIR spectroscopy could serve as a reliable tool to assist in bone species determination and also has great potential in real forensic cases with natural conditions.

Discovery of markers for discriminating the age of cultivated ginseng by using UHPLC-QTOF/MS coupled with OPLS-DA

BackgroundGinseng (Ginseng Radix et Rhizoma, Panax ginseng C.A. Meyer) is gaining more publicity in modern society due to its health benefit and huge value in market. In the practice of grading and pricing of ginseng, the age is one of the major factor influencing the price and grade of ginseng. Therefore, the age discrimination is an important task for the quality control of ginseng. However, the traditional morphological methods are too subjective to be reproductive in discrimination. PurposeTo establish a method that can discriminate the ginseng samples with different cultivation years. Study DesignTo analyze the correlation between chemical compositions and cultivation years of cultivated ginseng samples of different age and thus discover potential quality marker (Q-marker) for discriminating the age of cultivated ginseng. MethodsIn the present study, the ultra-high performance liquid chromatography coupled with the quadrupole-time of flight mass spectrometry (UHPLC-QTOF/MS) were utilized for the age discrimination and marker discovery. A statistical data processing procedure was established to screen markers and reduce the false positive rate. ResultsThe results showed that the ginseng samples from 2- to 6-year-old could be well separated in the orthogonal projections on the latent structure - discrimination analysis (OPLS-DA) using the markers screened by the established statistical procedure, which could reduce approximately 20% of the insignificant markers and false positive discoveries. Ultimately, more than 50 compounds contributing to the age discrimination were identified including one new compound (malonylginsenoside). One negative marker (1038.4825@8.98) was discovered for the 2-year-old ginseng, and an equation was established to effectively predict the age of 3- to 6-year-old of ginseng. ConclusionThe constructed method can discriminate the ginseng samples with different cultivation years and is a complement to the traditional discrimination method of ginseng age.

Detection and Identification of Six Monilinia spp. Causing Brown Rot Using TaqMan Real-Time PCR from Pure Cultures and Infected Apple Fruit

Brown rot is a severe disease affecting stone and pome fruit. This disease was recently confirmed to be caused by the following six closely related species: Monilinia fructicola, M. laxa, M. fructigena, Monilia polystroma, M. mumecola, and M. yunnanensis. Because of differences in geographic distributions, some of these species are important quarantine pathogens in certain countries. In this study, we developed TaqMan real-time polymerase chain reaction (PCR) assays to detect and identify the six species. Primer pairs and probes were designed for Monilinia fructicola, M. fructigena, M. laxa, and Monilia polystroma based on sequence differences in the laccase-2 genes. Additionally, based on sequence differences in the elongation factor genes, primer pairs and probes were designed for Monilia mumecola and M. yunnanensis. The real-time PCR assays were able to specifically identify the target pathogens, with detection limits of 10 to 100 fg of DNA, which is equivalent to one to seven conidia. The assays were also able to detect the target pathogens in a mixed DNA sample comprising all six Monilinia spp. and related species. The real-time PCR assays accurately detected target fungi from infected apple fruit. Furthermore, the identification results were consistent with those of traditional morphological methods.

Bioassessment of a Drinking Water Reservoir Using Plankton: High Throughput Sequencing vs. Traditional Morphological Method

Drinking water safety is increasingly perceived as one of the top global environmental issues. Plankton has been commonly used as a bioindicator for water quality in lakes and reservoirs. Recently, DNA sequencing technology has been applied to bioassessment. In this study, we compared the effectiveness of the 16S and 18S rRNA high throughput sequencing method (HTS) and the traditional optical microscopy method (TOM) in the bioassessment of drinking water quality. Five stations reflecting different habitats and hydrological conditions in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia, were sampled May 2016. Non-metric multi-dimensional scaling (NMDS) analysis showed that plankton assemblages varied among the stations and the spatial patterns revealed by the two methods were consistent. The correlation between TOM and HTS in a symmetric Procrustes analysis was 0.61, revealing overall good concordance between the two methods. Procrustes analysis also showed that site-specific differences between the two methods varied among the stations. Station Heijizui (H), a site heavily influenced by two tributaries, had the largest difference while station Qushou (Q), a confluence site close to the outlet dam, had the smallest difference between the two methods. Our results show that DNA sequencing has the potential to provide consistent identification of taxa, and reliable bioassessment in a long-term biomonitoring and assessment program for drinking water reservoirs.

The application of frontal sinus index and frontal sinus area in sex estimation based on lateral cephalograms among Han nationality adults in Xinjiang

The frontal sinus, due to its unique anatomical features, has become an important element in research for individual identification. Previous studies have demonstrated the use of frontal sinus as an indicator for sex discrimination; however, the sex discrimination rate using frontal sinus was lower compared to that using the traditional morphological methods. In order to improve the sex discrimination percentage, we developed a new method involving the measurement of the frontal sinus index and frontal sinus area from lateral cephalogram radiographs. In this study, 475 digital lateral cephalograms of adult Han citizens from Xinjiang were included. The maximum height, depth, and area of the frontal sinus were calculated using the NemoCeph NX software. The frontal sinus index (ratio of the maximum height to the depth of frontal sinus) was also computed. Statistical analysis results showed significant differences in the frontal sinus index and area between males and females. Discriminant function equation derived from this study differentiated between sexes with 76.6% accuracy. The results demonstrated that the use of frontal sinus index and area for sex discrimination was more accurate than using the frontal sinus index alone.

Wildlife parasitology in Australia: past, present and future

Wildlife parasitology is a highly diverse area of research encompassing many fields including taxonomy, ecology, pathology and epidemiology, and with participants from extremely disparate scientific fields. In addition, the organisms studied are highly dissimilar, ranging from platyhelminths, nematodes and acanthocephalans to insects, arachnids, crustaceans and protists. This review of the parasites of wildlife in Australia highlights the advances made to date, focussing on the work, interests and major findings of researchers over the years and identifies current significant gaps that exist in our understanding. The review is divided into three sections covering protist, helminth and arthropod parasites. The challenge to document the diversity of parasites in Australia continues at a traditional level but the advent of molecular methods has heightened the significance of this issue. Modern methods are providing an avenue for major advances in documenting and restructuring the phylogeny of protistan parasites in particular, while facilitating the recognition of species complexes in helminth taxa previously defined by traditional morphological methods. The life cycles, ecology and general biology of most parasites of wildlife in Australia are extremely poorly understood. While the phylogenetic origins of the Australian vertebrate fauna are complex, so too are the likely origins of their parasites, which do not necessarily mirror those of their hosts. This aspect of parasite evolution is a continuing area for research in the case of helminths, but remains to be addressed for many other parasitic groups.

Performance of VITEK mass spectrometry V3.0 for rapid identification of clinical Aspergillus fumigatus in different culture conditions based on ribosomal proteins.

Fast and accurate discrimination of Aspergillus fumigatus is significant, since misidentification may lead to inappropriate clinical therapy. This study assessed VITEK mass spectrometry (MS) V3.0 for A. fumigatus identification using extracted fungal ribosomal proteins. A total of 52 isolates preliminarily identified as A. fumigatus by traditional morphological methods were inoculated in three different culture media and cultured at two different temperatures. The specific spectral fingerprints of different culture time points (48, 72, 96, and 120 h) were obtained. Of all strains, 88.5% (46/52) were discriminated as A. fumigatus, while the remaining 11.5% (6/52) produced results inconsistent with morphological analysis. Molecular sequencing, as a reference method for species identification, was used to validate the morphological analysis and matrix-assisted laser desorption/ionization time of flight MS. Chi-square tests (χ2 test, P=0.05) demonstrated that the culture medium and incubation temperature had no effects on identification accuracy; however, identification accuracy of the strains in the 48-h group was lower than that in other groups. In addition, we found that ribosomal proteins extracted from A. fumigatus can be stored in different environments for at least 1 week, with their profiles remaining stable and strain identification results showing no change. This is beneficial for medical institutions with no mass spectrometer at hand. Overall, this study showed the powerful ability of VITEK MS V 3.0 in identifying A. fumigatus.

Non-invasive genetics outperforms morphological methods in faecal dietary analysis, revealing wild boar as a considerable conservation concern for ground-nesting birds.

Capercaillie (Tetrao urogallus) and other grouse species represent conservation concerns across Europe due to their negative abundance trends. In addition to habitat deterioration, predation is considered a major factor contributing to population declines. While the role of generalist predators on grouse predation is relatively well known, the impact of the omnivorous wild boar has remained elusive. We hypothesize that wild boar is an important predator of ground-nesting birds, but has been neglected as a bird predator because traditional morphological methods underestimate the proportion of birds in wild boar diet. To distinguish between different mammalian predator species, as well as different grouse prey species, we developed a molecular method based on the analysis of mitochondrial DNA that allows accurate species identification. We collected 109 wild boar faeces at protected capercaillie leks and surrounding areas and analysed bird consumption using genetic methods and classical morphological examination. Genetic analysis revealed that the proportion of birds in wild boar faeces was significantly higher (17.3%; 4.5×) than indicated by morphological examination (3.8%). Moreover, the genetic method allowed considerably more precise taxonomic identification of consumed birds compared to morphological analysis. Our results demonstrate: (i) the value of using genetic approaches in faecal dietary analysis due to their higher sensitivity, and (ii) that wild boar is an important predator of ground-nesting birds, deserving serious consideration in conservation planning for capercaillie and other grouse.

The diversity and structure of marine protists in the coastal waters of China revealed by morphological observation and 454 pyrosequencing

Pyrosequencing of the 18S rRNA gene has been widely adopted to study the eukaryotic diversity in various types of environments, and has an advantage over traditional morphology methods in exploring unknown microbial communities. To comprehensively assess the diversity and community composition of marine protists in the coastal waters of China, we applied both morphological observations and high-throughput sequencing of the V2 and V3 regions of 18S rDNA simultaneously to analyze samples collected from the surface layer of the Yellow and East China Seas. Dinoflagellates, diatoms and ciliates were the three dominant protistan groups as revealed by the two methods. Diatoms were the first dominant protistan group in the microscopic observations, with Skeletonema mainly distributed in the nearshore eutrophic waters and Chaetoceros in higher temperature and higher pH waters. The mixotrophic dinoflagellates, Gymnodinium and Gyrodinium, were more competitive in the oligotrophic waters. The pyrosequencing method revealed an extensive diversity of dinoflagellates. Chaetoceros was the only dominant diatom group in the pyrosequencing dataset. Gyrodinium represented the most abundant reads and dominated the offshore oligotrophic protistan community as they were in the microscopic observations. The dominance of parasitic dinoflagellates in the pyrosequencing dataset, which were overlooked in the morphological observations, indicates more attention should be paid to explore the potential role of this group. Both methods provide coherent clustering of samples. Nutrient levels, salinity and pH were the main factors influencing the distribution of protists. This study demonstrates that different primer pairs used in the pyrosequencing will indicate different protistan community structures. A suitable marker may reveal more comprehensive composition of protists and provide valuable information on environmental drivers.

太平洋克拉里昂-克利伯顿断裂带嘴刺目线虫多样性

PDF HTML阅读 XML下载 导出引用 引用提醒 太平洋克拉里昂-克利伯顿断裂带嘴刺目线虫多样性 DOI: 10.5846/stxb201509181920 作者: 作者单位: 1 国家海洋局第二海洋研究所，杭州，310012; 2浙江大学生命科学学院，杭州，310058,国家海洋局第二海洋研究所,国家海洋局第二海洋研究所,浙江大学生命科学学院,国家海洋局第二海洋研究所,国家海洋局第二海洋研究所 作者简介: 通讯作者: 中图分类号: 基金项目: 国际海域资源调查与开发“十二五”课题（DY125-14-E-02；DY125-22-QY-29） Nematode (Enoplida) diversity in sediment samples collected from the Clarion-Clipperton Fracture Zone Author: Affiliation: 1 Second Institute of Oceanography, Hangzhou, 310058, China; 2 College of life science, Zhejiang University, Hangzhou, 310012, China,The Second Institute of Oceanography,SOA,The Second Institute of Oceanography,College of life science, Zhejiang University,The Second Institute of Oceanography,SOA,The Second Institute of Oceanography,SOA Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:从太平洋深海克拉里昂-克利伯顿断裂带（Clarion-Clipperton fracture zone，简称CC区）4个站位采集的深海沉积物样品中检出26条嘴刺目（Enoplida）线虫个体。综合应用形态学和分子生物学方法，共鉴定嘴刺目线虫6科8属，其中尖口线虫科（Oxystominidae）个体数量最多，占总数的57.7%，其次为前感线虫科（Anticomidae，19.2%）、光皮线虫科（Phanodermatidae，7.7%）、钩线虫科（Oncholaimidae，7.7%）、烙线虫科（Ironidae，3.8%）和矛线虫科（Enchelidiidae，3.8%）。科、属组成与相邻站点同期采样所获的线虫近似，而丰度组成比例有所差异。分子生物学方法获得了线虫rRNA基因序列16条，经GenBank数据库比对，其与已有的序列相似性范围为94%-99%，以此为依据可确定到科的水平和大部分属的水平（84.6%）。DNA条形码比对结果和形态学鉴定结果有较高一致性，表明分子条形码技术可作为深海线虫鉴定的有效手段。系统发育分析结果显示，基于18S和28S rRNA基因序列，采用不同方法构建系统发育树，其分支结构基本一致；钩线虫科和矛线虫科聚类在一起，光皮线虫科和前感线虫科聚类在一起，显示出彼此间较近的遗传关系。 Abstract:Marine free-living nematodes (Phylum Nematoda) are widespread and abundant in marine sediments, often representing 70%-90% of the benthic metazoans. However, marine nematode taxonomy is severely underdeveloped, and about only 4,000 species of free-living marine nematodes have been described. Nematode identification by using traditional morphological methods is time consuming and expensive. Some marine nematodes are small, displaying similar morphological characters and are difficult to identify by traditional methods. Molecular technology, or "barcoding," offers the potential of a fast and objective way of species identification. The small and large subunit ribosomal DNA (SSU rDNA and LSU rDNA) gene-based phylogenetic analysis is a powerful tool for clarifying evolutionary relationships among nematode taxa. The order Enoplida is one of the most important groups of marine nematodes. Many enoplids are possibly active predators, and play important ecological roles in marine environments. Here we reported the isolation of 26 nematodes, belonging to Enoplida, from sediment samples collected at four sites in the Clarion-Clipperton Fracture Zone of the Pacific Ocean. The specimens were preserved in DESS solution (20% dimethyl sulphoxide, 0.25 mol/L disodium EDTA pH 8.0, saturated with NaCl) immediately after collection. Each sediment sample was rinsed through a 38-μm sieve using filtered seawater, and extracted using the Ludox flotation method. Nematodes were placed on temporary slides and observed using a Leica DM5500 microscope. After image capturing, each specimen was washed, cut into several pieces, transferred into micro-centrifuge tubes, and digested with Proteinase K. A series of frozen specimens was subsequently thawed and subjected to PCR amplification of the 18S rRNA gene and D3 expansion segments of the 28S rRNA gene. Sequences were analyzed and compared with published data from GenBank by means of a BLAST search. Phylogenetic trees were constructed using the neighbor-joining, maximum likelihood, and maximum parsimony methods with the MEGA5 program package, after multiple alignment of the data by CLUSTAL W. Based on morphological and molecular analyses, these 26 nematodes were classified into six families and eight genera, among which Oxystominidae was the most abundant family, accounting for 57.7%. The other families included Anticomidae (19.2%), Phanodermatidae (7.7%), Oncholaimidae (7.7%), Ironidae (3.85%), and Enchelidiidae (3.85%). At the family and genus level, the community composition at adjacent sites during the same period showed similar results, but the abundance was different. Sixteen sequences of rRNA gene were obtained in the present study and their similarity to the sequences in GenBank ranged from 94 to 99%. According to the results from BLAST, all sequences could be identified at the level of family, while 84.6% of the 16 sequences could be identified at the level of genus. The results from morphological and molecular analysis showed high consistency, which suggested that molecular barcoding is an efficient method to identify deep-sea nematodes. Phylogenetic trees constructed from the sequences of 18S and 28S rRNA gene showed similar topological structures; the species of Oncholaimidae and Enchelidiidae were clustered into one group, whereas those of Phanodermatidae and Anticomidae were clustered into another group, indicating their close genetic relationships. 参考文献 相似文献 引证文献

Species identification of partial fish larvae and juveniles in Fujian coastal areas based on cytochrome C oxidase subunit I barcoding

PDF HTML阅读 XML下载 导出引用 引用提醒 基于CO I基因的福建近海部分仔稚鱼DNA条形码分析 DOI: 作者: 作者单位: 福建省水产研究所, 福建省海洋生物增养殖与高值化利用重点实验室, 福建 厦门 361013 作者简介: 徐春燕(1986-),女,硕士,助理研究员,主要从事渔业资源生物学及生态学研究.E-mail:xuchunyan218@126.com 通讯作者: 中图分类号: S93 基金项目: 福建省省属公益类科研院所基本科研专项（2015R1003-5）；福建省海洋生物增养殖与高值化利用重点实验室开放课题（2016fjscq04）；闽台重要海洋生物资源高值化开发技术公共服务平台（2014FJPT01）；福建重要海洋经济生物种质库与资源高效开发技术公共服务平台（14PZY017NF17）. Species identification of partial fish larvae and juveniles in Fujian coastal areas based on cytochrome C oxidase subunit I barcoding Author: Affiliation: Fisheries Research Institute of Fujian;Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen 361013, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为研究DNA条形码技术在遭遇瓶颈的仔稚鱼种类鉴定中的适用性，2015年7月17-20日采集福建近海仔稚鱼样品，并挑选80尾进行DNA条形码分析。获得仔稚鱼的CO I基因序列73条，鉴定仔稚鱼26种，隶属于7目22科25属，另有5个物种仅鉴定到属，2个物种仅鉴定到科。种内平均遗传距离为0.0023，属内种间遗传距离为0.1797，约为种内遗传距离的78倍，说明利用CO I基因可以进行有效的仔稚鱼物种鉴定。科内属间、目内科间的遗传距离分别为0.1937、0.2420，遗传距离随着分类阶元的提高而增大。在系统进化树的分析中，同一种类的不同个体都聚在一支，所有物种都分别聚为独立的一支，这些物种都能有效区分开来。以上结果表明，线粒体CO I基因作为DNA条形码可以实现仔稚鱼的物种鉴定，且较多能鉴定到种的水平。 Abstract:Fish eggs, larvae, and juveniles are important food sources for fish populations. Correct identification of fish eggs, larvae, and juveniles can let us understand which species are spawning where and when, their hatching and nursery grounds, and their possible migration routes during their early life history. At present, fish larval and juvenile identification mostly relies on morphological characters. But since different species often share similar characters and species change greatly during their early development stages, identification of fish larvae and juveniles is very hard, most of which can only be identified to the family or genus level, except for a few fish juveniles that can be identified to species. Moreover, because traditional morphological methods rely too much on personal experience and observation methods, it is easy to misidentify fish larvae and juveniles and difficult to identify to the genus or species level. In view of the limitations of traditional morphological methods, DNA barcode techniques could be a rapid tool to survey many uncertain species, species composition, and cryptic species and to distinguish morphologically similar species. To study the applicability of this technique to identify fish larvae and juveniles, samples were collected in Fujian coastal areas from July 17 to 20, 2015, and 80 samples were selected for DNA barcoding analysis. A total of 73 valid cytochrome C oxidase subunit I (CO I) gene sequences of fish larvae and juveniles in Fujian coastal areas were obtained. Five species were identified to the level of genus, two were identified to the level of family, and another 26 species were identified to the level of species. The results showed that the average Kimura-2-parameter (K2P) distances within species, genus, family, and order were 0.0023, 0.1797, 0.1937, and 0.2420, respectively. The interspecific genetic distance was much larger than the intraspecific distance, and K2P genetic distance values increased with taxonomic level. All sequences formed species units in a neighbor-joining phylogenetic tree, indicating that the DNA barcode can be used to identify these 33 species. Consequently, CO I barcoding is one of the useful tools to identify fish larvae and juveniles. However, this test highlights the limitations of DNA barcoding. The neighbor-joining tree cannot analyze cluster relations clearly above the taxonomic level of family, which corresponds to the slower-increasing trend of genetic distance values with the higher taxa. This means that CO I barcoding is only suitable for phylogenetic analysis of lower taxa, and is not applicable for species identification of higher taxa. Four sequences having high similarity (greater than 98%) with many species in the database were identified only to genus ( sp.). That indicates that some fish species are similar not only in shape but also in CO I sequences, and sequence identification cannot be done using only CO I barcoding. We should strengthen the research of multi-gene barcode technology in order to overcome the deficiency of the single CO I gene sequence. Another sequence, limited by the number of sequences that can be used in the DNA database, with a maximum similarity between 85%-86%, was identified to the level of family. It is suggested to further improve the sequence quantity and quality of the DNA barcode database, so as to let it be more useful for species identification. 参考文献 相似文献 引证文献

Advances in Fungal Phylogenomics and Their Impact on Fungal Systematics.

In the past decade, advances in next-generation sequencing technologies and bioinformatic pipelines for phylogenomic analysis have led to remarkable progress in fungal systematics and taxonomy. A number of long-standing questions have been addressed using comparative analysis of genome sequence data, resulting in robust multigene phylogenies. These have added to, and often surpassed traditional morphology or single-gene phylogenetic methods. In this chapter, we provide a brief history of fungal systematics and highlight some examples to demonstrate the impact of phylogenomics on this field. We conclude by discussing some of the challenges and promises in fungal biology posed by the ongoing genomics revolution.

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae).

Premise of the StudyThe internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista. This study addresses the comparative potential of ITS datasets (ITS1, ITS2 and concatenated) in resolving the underlying morphological disparity in the highly complex genera, to assess their discriminatory power as potential barcode candidates in Cassiinae.MethodologyA combination of experimental data and an in-silico approach based on threshold genetic distances, sequence similarity based and hierarchical tree-based methods was performed to decipher the discriminating power of ITS datasets on 18 different species of Cassiinae complex. Lab-generated sequences were compared against those available in the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum likelihood and Bayesian inference (BI) methods of gene and species tree reconciliation with bootstrapping. DNA barcoding gap was realized based on the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.Principal FindingsBased on the K2P distance, significant divergences between the inter- and intra-specific genetic distances were observed, while the presence of a DNA barcoding gap was obvious. The ITS1 region efficiently identified 81.63% and 90% of species using TaxonDNA and BI methods, respectively. The PWG-distance method based on simple pairwise matching indicated the significance of ITS1 whereby highest number of variable (210) and informative sites (206) were obtained. The BI tree-based methods outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses.ConclusionThe reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

Specific Detection of the Root-Lesion Nematode Pratylenchus scribneri Using Conventional and Real-Time PCR.

Pratylenchus scribneri is a plant-parasitic root-lesion nematode causing economic damage to various crops worldwide. Identifying root-lesion nematodes to species using traditional morphological methods is an arduous task requiring extensive training on nematode taxonomy and years of experience. Thus, molecular methods for P. scribneri detection and identification were developed. Conventional and real-time polymerase chain reaction (PCR) assays with new species-specific primers were used in this study, which exclusively amplified DNA of P. scribneri but not DNA from other Pratylenchus spp. or non-Pratylenchus spp. tested. Compared with conventional PCR that was able to detect an equivalent to 1/4 of the DNA of a single nematode, real-time PCR was more sensitive and could amplify an equivalent to 1/128 of the DNA of one nematode. Both conventional and real-time PCR assays successfully identified P. scribneri and distinguished it from P. penetrans and P. neglectus isolated from field samples collected from various locations in North Dakota and Minnesota. The Blast-search based on the sequence information confirmed the reliability of the PCR assays for species identification. This is the first report of P. scribneri identification using a real-time PCR assay. The developed PCR assays are suitable for use in diagnostic laboratories and detection of field infestations with this nematode species.

The use of shape analysis to differentiate between the mandibles of four economically important tephritid species

AbstractThe three fruit fly species (Diptera: Tephritidae) of economic importance that are most commonly intercepted during inspections of fruit for export at the Plant Quarantine Station of the Department of Agriculture Forestry and Fisheries in Stellenbosch, South Africa, are Ceratitis capitata, Ceratitis rosa and Ceratitis cosyra. A fourth fruit fly species of economic importance in South Africa which was recently declared present in the northern and north‐eastern parts of the country is Bactrocera dorsalis. Bactrocera dorsalis is absent in other areas of the country, including the Western Cape Province. The larval stage of fruit flies is the most commonly intercepted life stage, and identification of this stage using traditional morphological methods such as identification keys is difficult. This study investigates the use of shape analysis, a morphometric method, to identify the third instar larvae of four tephritid species commonly intercepted in fruit destined for export. Larval specimens of laboratory reared B. dorsalis, C. capitata, C. rosa s.s. and C. cosyra were used. The mandibles of third instar larvae of all species were dissected out, dehydrated and mounted in Euparal. Images of the mandibles were captured and analysed using elliptical Fourier descriptors (in the SHAPE v.1.3 analysis programme). According to the cumulative eigenvalues, the first two principal components (PCs) contributed the most (65%) to the shape change. The canonical variate analysis showed that the first PC separates C. rosa s.s. and C. cosyra from C. capitata and B. dorsalis. Ceratitis capitata and B. dorsalis were separated by the second PC. This study showed that morphometrics, in the form of shape analysis of the mandibles, can be used in combination with measurements of the mandibles to distinguish between third instar larvae of B. dorsalis, C. capitata, C. rosa s.s. and C. cosyra.

Research progress in metabolic and receptor-like nuclear imaging agents for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) commonly presents with high morbidity and mortality, and early staging diagnosis and timely treatment is pivotal to prolonging patients' survival time. Compared with traditional morphological imaging methods such as ultrasound, computed tomography (CT), and magnetic resonance imaging (MRI), functional imaging methods like single-photon emission computed tomography (SPECT) and positron emission tomography (PET) are playing an increasingly important role in the early diagnosis, efficacy assessment, prognostic evaluation, and treatment planning for HCC, thanks to their higher sensitivity at a molecular level by using various radiopharmaceuticals.

A way to interconnect the multispectral images for improved vision systems by using the methods of diffusive morphology

A new way to interconnect multispectral images by using the methods of diffusive morphology are presented for implementing improved vision systems in aviation. In contrast to the traditional morphological methods, in the presented approach, it is not necessary to segment in advance the image for describing its shape and it ensures strong resistance against noise and distortions. Procedures for two- and three-channel image interconnection are developed based on diffusive morphological filtration. How to use them by using the image pyramid is also presented. A promising prototype of an improved vision system is described. The interconnecting algorithms are processed experimentally by using the multispectral data collected during an aviation experiment by using the described prototype.

Taxonomic status of a population of Gymoncypris waddelli Regan, 1905(Cypriniformes: Schizothoracinae) distributed in Pengqu River, Tibet, China.

Gymnocypris waddelli, a highland cold-water fish, is distributed among rivers and lakes of the southern Qinghai-Tibet Plateau. Although previously described as G. waddelli, specimens from the Pengqu River are morphologically distinguishable from those from Lake Yamzhog Yumco, which is the type locality of G. waddelli. We investigated morphological variations of G. waddelli specimens from Pengqu River and Lake Yamzhog Yumco using not only traditional morphological methods but also newly-developed geometric morphometric analysis; furthermore, mitochondrial Cytochrome b (Cyt b) gene analysis was employed to explore the phylogenetic position of the Pengqu River population. Our morphological analyses suggested that G. waddelli from the Pengqu River had an obtuse snout, nearly straight oral fissure, shorter lower jaw than upper jaw, broad mouth and sparse inside gill rakers of the first arch relative to the Lake Yamzhog Yumco population. The strongly supported monophyly of Pengqu population according to mitochondrial datasets was obtained, indicating genetic differences between Pengqu River and Lake Yamzhog Yumco populations. Given their substantial genetic and morphological divergence, specimens from Pengqu River warrant recognition as a distinct species, here described and named Gymnocypris pengquensis.

Sex discrimination of mastoid process by anthropometric measurements using multidetector computed tomography in Egyptian adult population

IntroductionSex identification of different skeletal remains has been defiance for many forensic studies. Mastoid process of the skull has drawn great attention from many researchers. Sex differences of the mastoid process are investigated using traditional morphological and metric methods. AimThe aim of the present study was to use multidetector computed tomography (MDCT) to estimate sex from measuring the mastoid process of adult individuals. Subjects and methodsEighty adult subjects (40 males and 40 females) of the Egyptian population were included in the present study with a mean age of 32.8+12.98 and 28.9+10.1, respectively. Nine mastoid measurements were obtained on the mastoid and were subjected to statistical analysis using SPSS version 16. Accuracy of MDCT and cut-off points to estimate sex from mastoid process were then obtained. ResultsAll mastoid dimensions except mastoid angles were larger in males than in females. Conventional mastoid height (cMH), oblique sagittal diameter (OSD) and mastoid volume with its three components, showed high accuracy (85–75%) in discriminating sex. As regards cMH and mastoid volume, the cutoff point was (30.15) with overall accuracy (85%) in cMH, whereas, in mastoid volume the cutoff point was (7.77) with overall accuracy of (75%). ConclusionIt was concluded that the conventional mastoid height (cMH), and oblique sagittal diameter (OSD) and mastoid volume were more accurate for sex discrimination in the Egyptian population.

Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Introduction and spread of invasive non-indigenous species (NIS) has been clearly recognized as a growing global problem in marine and coastal ecosystems. Early detection of NIS has been recognized as one of the first priorities and effective ways in management programs. However, the detection of an array of rare NIS based on traditional morphological methods represents enormous technical challenges in the marine realm, as numerous poorly studied organisms may be small and/or have insufficient morphological distinctive features. The use of DNA-based approaches has largely increased the detection accuracy and efficiency. Owing to many obvious advantages such as the high capacity to detect extremely low-abundance species and low cost per sequence, high-throughput sequencing (HTS)-based methods have been popularly proposed for early detection of marine NIS. Although HTS-based approaches have been approved robust for the census of NIS in aquatic ecosystems, especially for those present at extremely low abundance, many factors in experimental design and data collection can cause errors including both false negatives and false positives. Here we identify factors responsible for both error types, discuss causes and consequences, and propose possible solutions when utilizing HTS for early detection of NIS in marine and coastal ecosystems.