Light Detection and Ranging (LiDAR) technology has been widely used in forestry surveys in the form of airborne laser scanning (ALS), terrestrial laser scanning (TLS), and mobile laser scanning ...(MLS). The acquisition of important basic tree parameters (e.g., diameter at breast height and tree position) in forest inventory did not solve the problem of low measurement efficiency or weak GNSS signal under the canopy. A personal laser scanning (PLS) device combined with SLAM technology provides an effective solution for forest inventory under complex conditions with its light weight and flexible mobility. This study proposes a new method for calculating the volume of a cylinder using point cloud data obtained by a PLS device by fitting to a polygonal cylinder to calculate the diameter of the trunk. The point cloud data of tree trunks of different thickness were modeled using different fitting methods. The rate of correct tree trunk detection was 93.3% and the total deviation of the estimations of tree diameter at breast height (DBH) was -1.26 cm. The root mean square errors (RMSEs) of the estimations of the extracted DBH and the tree position were 1.58 cm and 26 cm, respectively. The survey efficiency of the personal laser scanning (PLS) device was 30m2/min for each investigator, compared with 0.91m2/min for the field survey. The test demonstrated that the PLS device combined with the SLAM algorithm provides an efficient and convenient solution for forest inventory.
Plant DNA barcoding: from gene to genome Li, Xiwen; Yang, Yang; Henry, Robert J. ...
Biological reviews of the Cambridge Philosophical Society,
February 2015, Letnik:
90, Številka:
1
Journal Article
Recenzirano
ABSTRACT
DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species; however, none of the available loci work across all species. ...Because single‐locus DNA barcodes lack adequate variations in closely related taxa, recent barcoding studies have placed high emphasis on the use of whole‐chloroplast genome sequences which are now more readily available as a consequence of improving sequencing technologies. While chloroplast genome sequencing can already deliver a reliable barcode for accurate plant identification it is not yet resource‐effective and does not yet offer the speed of analysis provided by single‐locus barcodes to unspecialized laboratory facilities. Here, we review the development of candidate barcodes and discuss the feasibility of using the chloroplast genome as a super‐barcode. We advocate a new approach for DNA barcoding that, for selected groups of taxa, combines the best use of single‐locus barcodes and super‐barcodes for efficient plant identification. Specific barcodes might enhance our ability to distinguish closely related plants at the species and population levels.
Conventional wet laboratory testing, validations, and synthetic procedures are costly and time-consuming for drug discovery. Advancements in artificial intelligence (AI) techniques have ...revolutionized their applications to drug discovery. Combined with accessible data resources, AI techniques are changing the landscape of drug discovery. In the past decades, a series of AI-based models have been developed for various steps of drug discovery. These models have been used as complements of conventional experiments and have accelerated the drug discovery process. In this review, we first introduced the widely used data resources in drug discovery, such as ChEMBL and DrugBank, followed by the molecular representation schemes that convert data into computer-readable formats. Meanwhile, we summarized the algorithms used to develop AI-based models for drug discovery. Subsequently, we discussed the applications of AI techniques in pharmaceutical analysis including predicting drug toxicity, drug bioactivity, and drug physicochemical property. Furthermore, we introduced the AI-based models for de novo drug design, drug-target structure prediction, drug-target interaction, and binding affinity prediction. Moreover, we also highlighted the advanced applications of AI in drug synergism/antagonism prediction and nanomedicine design. Finally, we discussed the challenges and future perspectives on the applications of AI to drug discovery.
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Chen and colleagues reviewed the applications of AI in drug discovery from the following aspects including data resources, molecular descriptors, and representative applications of AI in drug discovery. The challenges and perspectives for the applications of AI in drug discovery and development were discussed as well.
Numerous adverse reactions have arisen following the use of inaccurately identified medicinal plant ingredients, resulting in conditions such as aristolochic acid nephropathy and herb-induced ...poisoning. This problem has prompted increased global concern over the safety of herbal medicines. DNA barcoding, a technique aiming at detecting species-specific differences in a short region of DNA, provides a powerful new tool for addressing this problem. A preliminary system for DNA barcoding herbal materials has been established based on a two-locus combination of ITS2+psbA–trnH barcodes. There are 78,847 sequences belonging to 23,262 species in the system, which include more than 95% of crude herbal drugs in pharmacopeia, such as those of China, Japan, Korea, India, USA, and Europe. The system has been widely used in traditional herbal medicine enterprises. This review summarizes recent key advances in the DNA barcoding of medicinal plant ingredients (herbal materia medica) as a contribution towards safe and efficacious herbal medicines.
The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research ...applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.
Reasonable forest fire management measures can effectively reduce the losses caused by forest fires and forest fire driving factors and their impacts are important aspects that should be considered ...in forest fire management. We used the random forest model and MODIS Global Fire Atlas dataset (2010~2016) to analyse the impacts of climate, topographic, vegetation and socioeconomic variables on forest fire occurrence in six geographical regions in China. The results show clear regional differences in the forest fire driving factors and their impacts in China. Climate variables are the forest fire driving factors in all regions of China, vegetation variable is the forest fire driving factor in all other regions except the Northwest region and topographic variables and socioeconomic variables are only the driving factors of forest fires in a few regions (Northwest and Southwest regions). The model predictive capability is good: the AUC values are between 0.830 and 0.975, and the prediction accuracy is between 70.0% and 91.4%. High fire hazard areas are concentrated in the Northeast region, Southwest region and East China region. This research will aid in providing a national-scale understanding of forest fire driving factors and fire hazard distribution in China and help policymakers to design fire management strategies to reduce potential fire hazards.
Adulterant herbal materials are a threat to consumer safety. In this study, we used DNA barcoding to investigate the proportions and varieties of adulterant species in traditional Chinese medicine ...(TCM) markets. We used a DNA barcode database of TCM (TCMD) that was established by our group to investigate 1436 samples representing 295 medicinal species from 7 primary TCM markets in China. The results indicate that ITS2 barcodes could be generated for most of the samples (87.7%) using a standard protocol. Of the 1260 samples, approximately 4.2% were identified as adulterants. The adulterant focused on medicinal species such as Ginseng Radix et Rhizoma (Renshen), Radix Rubi Parvifolii (Maomeigen), Dalbergiae odoriferae Lignum (Jiangxiang), Acori Tatarinowii Rhizoma (Shichangpu), Inulae Flos (Xuanfuhua), Lonicerae Japonicae Flos (Jinyinhua), Acanthopanacis Cortex (Wujiapi) and Bupleuri Radix (Chaihu). The survey revealed that adulterant species are present in the Chinese market, and these adulterants pose a risk to consumer health. Thus, regulatory measures should be adopted immediately. We suggest that a traceable platform based on DNA barcode sequences be established for TCM market supervision.
The complete chloroplast genome of
(Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The
cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and ...IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the
cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of
is inverted; this fact is consistent with the sequences of chloroplast genomes from three other
species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In
cpDNA, the
gene was found in the LSC region rather than the IR region, and the
pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between
and
were very slight. A phylogenetic analysis revealed a sister relationship between
and
. This study identified the unique characteristics of the
cp genome. These results offer valuable information for future research on
species identification and for the selective breeding of
with high pharmaceutical efficacy.
Summary
Danshen, Salvia miltiorrhiza Bunge, is one of the most widely used herbs in traditional Chinese medicine, wherein its rhizome/roots are particularly valued. The corresponding bioactive ...components include the tanshinone diterpenoids, the biosynthesis of which is a subject of considerable interest. Previous investigations of the S. miltiorrhiza transcriptome have relied on short‐read next‐generation sequencing (NGS) technology, and the vast majority of the resulting isotigs do not represent full‐length cDNA sequences. Moreover, these efforts have been targeted at either whole plants or hairy root cultures. Here, we demonstrate that the tanshinone pigments are produced and accumulate in the root periderm, and apply a combination of NGS and single‐molecule real‐time (SMRT) sequencing to various root tissues, particularly including the periderm, to provide a more complete view of the S. miltiorrhiza transcriptome, with further insight into tanshinone biosynthesis as well. In addition, the use of SMRT long‐read sequencing offered the ability to examine alternative splicing, which was found to occur in approximately 40% of the detected gene loci, including several involved in isoprenoid/terpenoid metabolism.
Significance Statement
Here, we combined NGS and SMRT sequencing to generate a more complete/full‐length S. miltiorrhiza transcriptome. Our study provides a general model for studying the full‐length transcriptome, alternative splicing, and the biosynthesis of active constituents in medicinal plants, as well as important information about the important Danshen constituent of traditional Chinese medicine more specifically.
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