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Article ; Online: Microbial perspective on the skin-gut axis and atopic dermatitis.

Qu, Bo / Zhang, Xue-Er / Feng, Haoyue / Yan, Bonan / Bai, Yingchun / Liu, Shanlin / He, Yuhua

2024 Volume 19, Issue 1, Page(s) 20220782

Abstract: Atopic dermatitis (AD) is a relapsing inflammatory skin condition that has become a global health issue with complex etiology and mounting prevalence. The association of AD with skin and gut microbiota has been revealed by virtue of the continuous ... ...

Abstract	Atopic dermatitis (AD) is a relapsing inflammatory skin condition that has become a global health issue with complex etiology and mounting prevalence. The association of AD with skin and gut microbiota has been revealed by virtue of the continuous development of sequencing technology and genomics analysis. Also, the gut-brain-skin axis and its mutual crosstalk mechanisms have been gradually verified. Accordingly, the microbiota-skin-gut axis also plays an important role in allergic skin inflammation. Herein, we reviewed the relationship between the microbiota-skin-gut axis and AD, explored the underlying signaling molecules and potential pathways, and focused on the potential mechanisms of probiotics, antimicrobial peptides (AMPs), coagulase-negative staphylococci transplantation, fecal microbiota transplantation, AMPs, and addition of essential fatty acids in alleviating AD, with the aim to provide a new perspective for targeting microbiota in the treatment of allergic skin inflammation.
Language	English
Publishing date	2024-04-13
Publishing country	Poland
Document type	Journal Article ; Review
ZDB-ID	2817958-4
ISSN	2391-5412 ; 2391-5412
ISSN (online)	2391-5412
ISSN	2391-5412
DOI	10.1515/biol-2022-0782
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: To bee, or not to bee? One leg is the question.

Cavill, Emily Louisa / Liu, Shanlin / Zhou, Xin / Gilbert, M Thomas P

Molecular ecology resources

2022 Volume 22, Issue 5, Page(s) 1868–1874

Abstract: Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, ... ...

Abstract	Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry-preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a "minimally destructive" method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry-preserved insects for future genomic studies.
MeSH term(s)	Animals ; Bees/genetics ; DNA/genetics ; Genome ; Genomics/methods ; Insecta/genetics ; Museums ; Sequence Analysis, DNA/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13578
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Article ; Online: Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico

Klimova, Anastasia / Rodríguez‐Estrella, Ricardo / Meng, Guanliang / Gutiérrez‐Rivera, Jesús Neftalí / Jimenez‐Jimenez, María Luisa / Liu, Shanlin

Diversity and Distributions. 2023 Mar., v. 29, no. 3 p.438-461

2023

Abstract: AIM: Desert springs or oases are the only permanent mesic environments in highly water‐limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they ...

Abstract	AIM: Desert springs or oases are the only permanent mesic environments in highly water‐limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases. LOCATION: Baja California Peninsula, Mexico. METHODS: Arthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales. RESULTS: Over 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities. MAIN CONCLUSIONS: Neutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.
Keywords	DNA barcoding ; anthropogenic activities ; arthropod communities ; arthropods ; biodiversity ; climate change ; community structure ; habitats ; invasive species ; latitude ; oases ; people ; seasonal variation ; shrublands ; Mexico
Language	English
Dates of publication	2023-03
Size	p. 438-461.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020139-4
ISSN	1472-4642 ; 1366-9516
ISSN (online)	1472-4642
ISSN	1366-9516
DOI	10.1111/ddi.13672
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Article: Tracing the origin of honey products based on metagenomics and machine learning

Liu, Shanlin / Lang, Dandan / Meng, Guanliang / Hu, Jiahui / Tang, Min / Zhou, Xin

Food chemistry. 2022 Mar. 01, v. 371

2022

Abstract: The adulteration of honey is common. Recently, High Throughput Sequencing (HTS)-based metabarcoding method has been applied successfully to pollen/honey identification to determine floral composition that, in turn, can be used to identify the ... ...

Abstract	The adulteration of honey is common. Recently, High Throughput Sequencing (HTS)-based metabarcoding method has been applied successfully to pollen/honey identification to determine floral composition that, in turn, can be used to identify the geographical origins of honeys. However, the lack of local references materials posed a serious challenge for HTS-based pollen identification methods. Here, we sampled 28 honey samples from various geographic origins without prior knowledge of local floral information and applied a machine learning method to determine geographical origins. The machine learning method uses a resilient backpropagation algorithm to train a neural network. The results showed that biological components in honey provided characteristic traits that enabled accurate geographic tracing for nearly all honey samples, confidently discriminating honeys to their geographic origin with >99% success rates, including those separated by as little as 39 km.
Keywords	DNA barcoding ; adulterated products ; algorithms ; food chemistry ; honey ; metagenomics ; pollen ; provenance
Language	English
Dates of publication	2022-0301
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2021.131066
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Article: To bee, or not to bee? One leg is the question

Cavill, Emily Louisa / Liu, Shanlin / Zhou, Xin / Gilbert, M. Thomas P.

Molecular ecology resources. 2022 July, v. 22, no. 5

2022

Abstract	Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry‐preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a “minimally destructive” method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry‐preserved insects for future genomic studies.
Keywords	DNA ; bees ; food webs ; genome ; genomics ; invertebrates ; museums ; pollination ; seed dispersal
Language	English
Dates of publication	2022-07
Size	p. 1868-1874.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406816-0
ISSN	1471-8286 ; 1755-098X
ISSN (online)	1471-8286
ISSN	1755-098X
DOI	10.1111/1755-0998.13578
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Automatic defect inspection of thin film transistor-liquid crystal display panels using robust one-dimensional Fourier reconstruction with non-uniform illumination correction.

Zhang, Tengda / Dong, Jingtao / Yang, Lei / Liu, Shanlin / Lu, Rongsheng

The Review of scientific instruments

2021 Volume 92, Issue 10, Page(s) 103701

Abstract: Automatic inspection of micro-defects of thin film transistor-liquid crystal display (TFT-LCD) panels is a critical task in LCD manufacturing. To meet the practical demand of online inspection of a one-dimensional (1D) line image captured by the line ... ...

Abstract	Automatic inspection of micro-defects of thin film transistor-liquid crystal display (TFT-LCD) panels is a critical task in LCD manufacturing. To meet the practical demand of online inspection of a one-dimensional (1D) line image captured by the line scan visual system, we propose a robust 1D Fourier reconstruction method with the capability of automatic determination of the period Δx of the periodic pattern of a spatial domain line image and the neighboring length r of the frequency peaks of the corresponding frequency domain line image. Moreover, to alleviate the difficulty in the discrimination between the defects and the non-uniform illumination background, we present an effective way to correct the non-uniform background using robust locally weighted smoothing combined with polynomial curve fitting. As a proof-of-concept, we built a line scan visual system and tested the captured line images. The results reveal that the proposed method is able to correct the non-uniform illumination background in a proper way that does not cause false alarms in defect inspection but also preserves complete information about the defects in terms of the brightness and darkness as well as the shape, indicating its distinct advantage in defect inspection of TFT-LCD panels.
Language	English
Publishing date	2021-10-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/5.0060636
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Article ; Online: Chromosome-level genome assembly of bean flower thrips Megalurothrips usitatus (Thysanoptera: Thripidae).

Ma, Ling / Liu, Qiaoqiao / Wei, Shujun / Liu, Shanlin / Tian, Li / Song, Fan / Duan, Yuange / Cai, Wanzhi / Li, Hu

Scientific data

2023 Volume 10, Issue 1, Page(s) 252

Abstract: Bean flower thrips Megalurothrips usitatus is a staple pest of cowpea and other legumes and causes dramatic economic losses. Its small size allows for easy concealment, and large reproductive capacity easily leads to infestations. Despite the importance ... ...

Abstract	Bean flower thrips Megalurothrips usitatus is a staple pest of cowpea and other legumes and causes dramatic economic losses. Its small size allows for easy concealment, and large reproductive capacity easily leads to infestations. Despite the importance of a genome in developing novel management strategies, genetic studies on M. usitatus remain limited. Thus, we generated a chromosome-level M. usitatus genome using a combination of PacBio long read and Hi-C technologies. The assembled genome was 238.14 Mb with a scaffold N50 of 13.85 Mb. The final genome was anchored into 16 pseudo-chromosomes containing 14,000 genes, of which 91.74% were functionally annotated. Comparative genomic analyses revealed that expanded gene families were enriched in fatty acid metabolism and detoxification metabolism (ABC transporters), and contracted gene families were strongly associated with chitin-based cuticle development and sensory perception of taste. In conclusion, this high-quality genome provides an invaluable resource for us to understand the thrips' ecology and genetics, contributing to pest management.
MeSH term(s)	Animals ; Flowers ; Phylogeny ; Thysanoptera/genetics ; Vigna ; Chromosomes, Insect ; Genome, Insect
Language	English
Publishing date	2023-05-03
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02164-5
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Article: The IMD pathway in Hemipteran: A comparative analysis and discussion

Ma, Li / Liu, Shanlin / Lu, Ping / Yan, Xizhong / Hao, Chi / Wang, Han / Wei, Jiufeng / Qie, Xingtao / Lu, Zhiqiang

Developmental and comparative immunology. 2022 Nov., v. 136

2022

Abstract: The evolutionary patterns of the genes in the IMD pathway in hemipterans were characterized and compared. The hemipteran insects were clustered into two groups. One group that encompasses whitefly, plant lice, and scale insect partially lacks the IMD ... ...

Abstract	The evolutionary patterns of the genes in the IMD pathway in hemipterans were characterized and compared. The hemipteran insects were clustered into two groups. One group that encompasses whitefly, plant lice, and scale insect partially lacks the IMD pathway and all antimicrobial peptide (AMP) genes, with the vast majority of IMD pathway and all AMP genes being absent in aphids. The reasons for the absence of the IMD pathway and AMP genes in hemipterans were analyzed based on aphids, in terms of fitness costs. In case of limited resources, aphids have to make a trade-off between the necessary costs such as clean food sources, the essential amino acids supplied by primary bacterial symbionts for survival, nutrients and/or protections against stress provided by secondary symbionts, and the high reproductive capacity, and the costs that do not increase the fitness. Obviously, aphids have to abandon the strong immune system, especially the AMPs and IMD pathway which is mainly against Gram-negative bacteria. The common ground shared with aphids may be the reason for the absence of the IMD pathway and AMP genes in other hemipteran insects.
Keywords	Aleyrodidae ; antimicrobial peptides ; immune system ; immunology ; reproductive performance ; scale insects ; symbionts
Language	English
Dates of publication	2022-11
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	752411-0
ISSN	1879-0089 ; 0145-305X
ISSN (online)	1879-0089
ISSN	0145-305X
DOI	10.1016/j.dci.2022.104513
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.

Meng, Guanliang / Li, Yiyuan / Yang, Chentao / Liu, Shanlin

Nucleic acids research

2019 Volume 47, Issue 11, Page(s) e63

Abstract: Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset ... ...

Abstract	Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.
MeSH term(s)	Animals ; Computational Biology/methods ; DNA, Mitochondrial/chemistry ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Genome, Mitochondrial/genetics ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Molecular Sequence Annotation ; Sequence Analysis, DNA/methods ; Software
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2019-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkz173
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Article ; Online: Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application.

Li, Bingyan / Duan, Yuange / Du, Zhenyong / Wang, Xuan / Liu, Shanlin / Feng, Zengbei / Tian, Li / Song, Fan / Yang, Hailin / Cai, Wanzhi / Lin, Zhonglong / Li, Hu

Nature communications

2024 Volume 15, Issue 1, Page(s) 1379

Abstract: Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit ... ...

Abstract	Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.
MeSH term(s)	Humans ; Animals ; Wasps/genetics ; China ; Selection, Genetic ; Aphids/genetics ; Genetic Variation ; Host-Parasite Interactions
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45631-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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